From 7d8de0a0358f5e61825ef610a752340036623988 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Tue, 24 Feb 2026 18:13:46 +1300 Subject: [PATCH] Update links to point to new Nextflow docs --- changelog/seqera-enterprise/v22.3.md | 2 +- changelog/seqera-enterprise/v22.4.md | 2 +- changelog/seqera-enterprise/v23.4.md | 2 +- changelog/seqera-enterprise/v25.1.md | 2 +- changelog/seqera-enterprise/v25.2.md | 6 +++--- changelog/seqera-enterprise/v25.3.1.md | 2 +- changelog/seqera-enterprise/v25.3.md | 2 +- docusaurus.config.js | 2 +- fusion_docs/guide/aws-eks.md | 2 +- fusion_docs/guide/gcp-batch.md | 2 +- fusion_docs/guide/gcp-gke.md | 2 +- fusion_docs/guide/local/aws-s3.md | 2 +- fusion_docs/guide/local/azure-blob.md | 2 +- fusion_docs/guide/local/google-cloud.md | 2 +- fusion_docs/guide/local/minio.md | 2 +- fusion_docs/guide/snapshots/configuration.md | 8 ++++---- fusion_docs/licensing.md | 4 ++-- fusion_docs/reference.md | 2 +- platform-cli-docs/docs/reference/pipelines.md | 2 +- platform-cli-docs/docs/reference/runs.md | 2 +- platform-cli-docs/overlays/tw-runs.md | 2 +- platform-cli-docs/overlays/tw-secrets-add.md | 2 +- platform-cloud/docs/compute-envs/aws-batch.md | 8 ++++---- platform-cloud/docs/compute-envs/azure-batch.md | 10 +++++----- .../docs/compute-envs/google-cloud-batch.md | 8 ++++---- platform-cloud/docs/compute-envs/hpc.md | 14 +++++++------- platform-cloud/docs/compute-envs/overview.md | 4 ++-- .../advanced-topics/manual-azure-batch-setup.md | 6 +++--- .../docs/getting-started/deployment-options.md | 2 +- platform-cloud/docs/getting-started/proteinfold.md | 2 +- .../quickstart-demo/launch-pipelines.md | 2 +- platform-cloud/docs/getting-started/rnaseq.md | 2 +- platform-cloud/docs/launch/advanced.md | 4 ++-- platform-cloud/docs/launch/cache-resume.mdx | 8 ++++---- platform-cloud/docs/launch/launchpad.md | 6 +++--- platform-cloud/docs/monitoring/overview.md | 2 +- platform-cloud/docs/pipelines/overview.md | 2 +- platform-cloud/docs/platform-cloud.md | 2 +- platform-cloud/docs/reports/overview.md | 8 ++++---- platform-cloud/docs/secrets/overview.md | 4 ++-- .../docs/supported_software/dragen/overview.md | 2 +- .../azure_troubleshooting.md | 4 ++-- .../docs/troubleshooting_and_faqs/nextflow.md | 10 +++++----- .../troubleshooting_and_faqs/troubleshooting.md | 2 +- platform-enterprise_docs/compute-envs/aws-batch.md | 8 ++++---- .../compute-envs/azure-batch.md | 10 +++++----- .../compute-envs/google-cloud-batch.md | 8 ++++---- platform-enterprise_docs/compute-envs/hpc.md | 4 ++-- platform-enterprise_docs/compute-envs/overview.md | 4 ++-- .../credentials/aws_registry_credentials.md | 2 +- .../credentials/azure_registry_credentials.md | 2 +- .../credentials/docker_hub_registry_credentials.md | 2 +- .../credentials/gitea_registry_credentials.md | 2 +- .../credentials/github_registry_credentials.md | 2 +- .../credentials/gitlab_registry_credentials.md | 2 +- .../credentials/google_registry_credentials.md | 2 +- .../credentials/quay_registry_credentials.md | 2 +- .../advanced-topics/manual-azure-batch-setup.md | 6 +++--- .../enterprise/configuration/wave.md | 2 +- .../getting-started/deployment-options.md | 2 +- .../getting-started/proteinfold.md | 2 +- .../quickstart-demo/launch-pipelines.md | 2 +- platform-enterprise_docs/getting-started/rnaseq.md | 2 +- platform-enterprise_docs/launch/advanced.md | 4 ++-- platform-enterprise_docs/launch/cache-resume.mdx | 8 ++++---- platform-enterprise_docs/launch/launchpad.md | 6 +++--- platform-enterprise_docs/monitoring/overview.md | 2 +- platform-enterprise_docs/pipelines/overview.md | 2 +- platform-enterprise_docs/platform-enterprise.md | 2 +- platform-enterprise_docs/reports/overview.md | 8 ++++---- platform-enterprise_docs/secrets/overview.md | 4 ++-- .../supported_software/dragen/overview.md | 2 +- .../azure_troubleshooting.md | 4 ++-- .../troubleshooting_and_faqs/nextflow.md | 8 ++++---- .../troubleshooting_and_faqs/troubleshooting.md | 2 +- .../compute-envs/altair-grid-engine.md | 4 ++-- .../version-22.4/compute-envs/altair-pbs-pro.md | 4 ++-- .../version-22.4/compute-envs/lsf.md | 4 ++-- .../version-22.4/compute-envs/moab.md | 4 ++-- .../version-22.4/compute-envs/overview.md | 2 +- .../version-22.4/compute-envs/slurm.md | 4 ++-- .../credentials/aws_registry_credentials.md | 2 +- .../credentials/azure_registry_credentials.md | 2 +- .../credentials/docker_hub_registry_credentials.md | 2 +- .../credentials/google_registry_credentials.md | 2 +- .../credentials/quay_registry_credentials.md | 2 +- .../version-22.4/faqs.md | 10 +++++----- .../version-22.4/getting-started/usage.md | 2 +- .../version-22.4/launch/advanced.md | 2 +- .../version-22.4/launch/launch-form.md | 4 ++-- .../version-22.4/secrets/overview.md | 2 +- .../supported_software/dragen/overview.md | 2 +- .../supported_software/fusion/fusion.md | 2 +- .../compute-envs/altair-grid-engine.md | 4 ++-- .../version-23.1/compute-envs/altair-pbs-pro.md | 4 ++-- .../version-23.1/compute-envs/aws-batch.md | 2 +- .../version-23.1/compute-envs/azure-batch.md | 2 +- .../compute-envs/google-cloud-batch.md | 2 +- .../version-23.1/compute-envs/hpc.md | 6 +++--- .../version-23.1/compute-envs/lsf.md | 4 ++-- .../version-23.1/compute-envs/moab.md | 4 ++-- .../version-23.1/compute-envs/overview.md | 2 +- .../version-23.1/compute-envs/slurm.md | 4 ++-- .../credentials/aws_registry_credentials.md | 2 +- .../credentials/azure_registry_credentials.md | 2 +- .../credentials/docker_hub_registry_credentials.md | 2 +- .../credentials/google_registry_credentials.md | 2 +- .../credentials/quay_registry_credentials.md | 2 +- .../version-23.1/enterprise/configuration/wave.md | 4 ++-- .../version-23.1/faqs.md | 12 ++++++------ .../getting-started/deployment-options.md | 2 +- .../version-23.1/getting-started/usage.md | 2 +- .../version-23.1/launch/advanced.md | 2 +- .../version-23.1/launch/launch-form.md | 4 ++-- .../version-23.1/secrets/overview.md | 2 +- .../supported_software/dragen/overview.md | 2 +- .../compute-envs/altair-grid-engine.md | 4 ++-- .../version-23.2/compute-envs/altair-pbs-pro.md | 4 ++-- .../version-23.2/compute-envs/aws-batch.md | 2 +- .../version-23.2/compute-envs/azure-batch.md | 2 +- .../compute-envs/google-cloud-batch.md | 2 +- .../version-23.2/compute-envs/hpc.md | 6 +++--- .../version-23.2/compute-envs/lsf.md | 4 ++-- .../version-23.2/compute-envs/moab.md | 4 ++-- .../version-23.2/compute-envs/overview.md | 2 +- .../version-23.2/compute-envs/slurm.md | 4 ++-- .../credentials/aws_registry_credentials.md | 2 +- .../credentials/azure_registry_credentials.md | 2 +- .../credentials/docker_hub_registry_credentials.md | 2 +- .../credentials/google_registry_credentials.md | 2 +- .../credentials/quay_registry_credentials.md | 2 +- .../version-23.2/enterprise/configuration/wave.md | 4 ++-- .../version-23.2/faqs.md | 12 ++++++------ .../getting-started/deployment-options.md | 2 +- .../version-23.2/getting-started/usage.md | 2 +- .../version-23.2/launch/advanced.md | 2 +- .../version-23.2/launch/launch-form.md | 4 ++-- .../version-23.2/secrets/overview.md | 2 +- .../supported_software/dragen/overview.md | 2 +- .../version-23.3/compute-envs/aws-batch.md | 6 +++--- .../version-23.3/compute-envs/azure-batch.md | 6 +++--- .../compute-envs/google-cloud-batch.md | 4 ++-- .../compute-envs/google-cloud-lifesciences.md | 2 +- .../version-23.3/compute-envs/hpc.md | 6 +++--- .../version-23.3/compute-envs/overview.md | 4 ++-- .../credentials/aws_registry_credentials.md | 2 +- .../credentials/azure_registry_credentials.md | 2 +- .../credentials/docker_hub_registry_credentials.md | 2 +- .../credentials/gitea_registry_credentials.md | 2 +- .../credentials/github_registry_credentials.md | 2 +- .../credentials/gitlab_registry_credentials.md | 2 +- .../credentials/google_registry_credentials.md | 2 +- .../version-23.3/credentials/overview.md | 2 +- .../credentials/quay_registry_credentials.md | 2 +- .../version-23.3/enterprise/configuration/wave.md | 4 ++-- .../version-23.3/faqs.md | 14 +++++++------- .../getting-started/deployment-options.md | 2 +- .../version-23.3/launch/advanced.md | 2 +- .../version-23.3/launch/cache-resume.mdx | 8 ++++---- .../version-23.3/launch/launchpad.md | 4 ++-- .../version-23.3/monitoring/overview.md | 2 +- .../version-23.3/platform-enterprise.md | 2 +- .../version-23.3/secrets/overview.md | 6 +++--- .../supported_software/dragen/overview.md | 2 +- .../version-23.4/compute-envs/aws-batch.md | 6 +++--- .../version-23.4/compute-envs/azure-batch.md | 6 +++--- .../compute-envs/google-cloud-batch.md | 6 +++--- .../compute-envs/google-cloud-lifesciences.md | 2 +- .../version-23.4/compute-envs/hpc.md | 6 +++--- .../version-23.4/compute-envs/overview.md | 4 ++-- .../credentials/aws_registry_credentials.md | 2 +- .../credentials/azure_registry_credentials.md | 2 +- .../credentials/docker_hub_registry_credentials.md | 2 +- .../credentials/gitea_registry_credentials.md | 2 +- .../credentials/github_registry_credentials.md | 2 +- .../credentials/gitlab_registry_credentials.md | 2 +- .../credentials/google_registry_credentials.md | 2 +- .../version-23.4/credentials/overview.md | 2 +- .../credentials/quay_registry_credentials.md | 2 +- .../version-23.4/enterprise/configuration/wave.md | 4 ++-- .../version-23.4/faqs.md | 14 +++++++------- .../getting-started/deployment-options.md | 2 +- .../quickstart-demo/launch-pipelines.mdx | 2 +- .../version-23.4/getting-started/rnaseq.mdx | 2 +- .../version-23.4/launch/advanced.md | 2 +- .../version-23.4/launch/cache-resume.mdx | 8 ++++---- .../version-23.4/launch/launchpad.md | 6 +++--- .../version-23.4/monitoring/overview.md | 2 +- .../version-23.4/platform-enterprise.md | 2 +- .../version-23.4/reports/overview.md | 8 ++++---- .../version-23.4/secrets/overview.md | 6 +++--- .../supported_software/dragen/overview.md | 2 +- .../version-24.1/compute-envs/aws-batch.md | 8 ++++---- .../version-24.1/compute-envs/azure-batch.md | 6 +++--- .../compute-envs/google-cloud-batch.md | 8 ++++---- .../compute-envs/google-cloud-lifesciences.md | 2 +- .../version-24.1/compute-envs/hpc.md | 6 +++--- .../version-24.1/compute-envs/overview.md | 4 ++-- .../credentials/aws_registry_credentials.md | 2 +- .../credentials/azure_registry_credentials.md | 2 +- .../credentials/docker_hub_registry_credentials.md | 2 +- .../credentials/gitea_registry_credentials.md | 2 +- .../credentials/github_registry_credentials.md | 2 +- .../credentials/gitlab_registry_credentials.md | 2 +- .../credentials/google_registry_credentials.md | 2 +- .../version-24.1/credentials/overview.md | 2 +- .../credentials/quay_registry_credentials.md | 2 +- .../version-24.1/enterprise/configuration/wave.md | 4 ++-- .../getting-started/deployment-options.md | 2 +- .../version-24.1/getting-started/proteinfold.mdx | 2 +- .../quickstart-demo/launch-pipelines.md | 2 +- .../version-24.1/getting-started/rnaseq.mdx | 2 +- .../version-24.1/launch/advanced.md | 4 ++-- .../version-24.1/launch/cache-resume.mdx | 8 ++++---- .../version-24.1/launch/launchpad.md | 6 +++--- .../version-24.1/monitoring/overview.md | 2 +- .../version-24.1/platform-enterprise.md | 2 +- .../version-24.1/reports/overview.md | 8 ++++---- .../version-24.1/secrets/overview.md | 6 +++--- .../supported_software/dragen/overview.md | 2 +- .../azure_troubleshooting.md | 4 ++-- .../troubleshooting_and_faqs/nextflow.md | 8 ++++---- .../troubleshooting_and_faqs/troubleshooting.md | 2 +- .../version-24.2/compute-envs/aws-batch.md | 8 ++++---- .../version-24.2/compute-envs/azure-batch.md | 10 +++++----- .../compute-envs/google-cloud-batch.md | 8 ++++---- .../compute-envs/google-cloud-lifesciences.md | 2 +- .../version-24.2/compute-envs/hpc.md | 6 +++--- .../version-24.2/compute-envs/overview.md | 4 ++-- .../credentials/aws_registry_credentials.md | 2 +- .../credentials/azure_registry_credentials.md | 2 +- .../credentials/docker_hub_registry_credentials.md | 2 +- .../credentials/gitea_registry_credentials.md | 2 +- .../credentials/github_registry_credentials.md | 2 +- .../credentials/gitlab_registry_credentials.md | 2 +- .../credentials/google_registry_credentials.md | 2 +- .../version-24.2/credentials/overview.md | 2 +- .../credentials/quay_registry_credentials.md | 2 +- .../advanced-topics/manual-azure-batch-setup.md | 6 +++--- .../version-24.2/enterprise/configuration/wave.md | 4 ++-- .../getting-started/deployment-options.md | 2 +- .../version-24.2/getting-started/proteinfold.mdx | 2 +- .../quickstart-demo/launch-pipelines.md | 2 +- .../version-24.2/getting-started/rnaseq.mdx | 2 +- .../version-24.2/launch/advanced.md | 4 ++-- .../version-24.2/launch/cache-resume.mdx | 8 ++++---- .../version-24.2/launch/launchpad.md | 6 +++--- .../version-24.2/monitoring/overview.md | 2 +- .../version-24.2/platform-enterprise.md | 2 +- .../version-24.2/reports/overview.md | 8 ++++---- .../version-24.2/secrets/overview.md | 6 +++--- .../supported_software/dragen/overview.md | 2 +- .../azure_troubleshooting.md | 4 ++-- .../troubleshooting_and_faqs/nextflow.md | 10 +++++----- .../troubleshooting_and_faqs/troubleshooting.md | 2 +- .../version-25.1/compute-envs/aws-batch.md | 8 ++++---- .../version-25.1/compute-envs/azure-batch.md | 10 +++++----- .../compute-envs/google-cloud-batch.md | 8 ++++---- .../compute-envs/google-cloud-lifesciences.md | 2 +- .../version-25.1/compute-envs/hpc.md | 6 +++--- .../version-25.1/compute-envs/overview.md | 4 ++-- .../credentials/aws_registry_credentials.md | 2 +- .../credentials/azure_registry_credentials.md | 2 +- .../credentials/docker_hub_registry_credentials.md | 2 +- .../credentials/gitea_registry_credentials.md | 2 +- .../credentials/github_registry_credentials.md | 2 +- .../credentials/gitlab_registry_credentials.md | 2 +- .../credentials/google_registry_credentials.md | 2 +- .../version-25.1/credentials/overview.md | 2 +- .../credentials/quay_registry_credentials.md | 2 +- .../advanced-topics/manual-azure-batch-setup.md | 6 +++--- .../version-25.1/enterprise/configuration/wave.md | 2 +- .../getting-started/deployment-options.md | 2 +- .../version-25.1/getting-started/proteinfold.mdx | 2 +- .../quickstart-demo/launch-pipelines.md | 2 +- .../version-25.1/getting-started/rnaseq.mdx | 2 +- .../version-25.1/launch/advanced.md | 4 ++-- .../version-25.1/launch/cache-resume.mdx | 8 ++++---- .../version-25.1/launch/launchpad.md | 6 +++--- .../version-25.1/monitoring/overview.md | 2 +- .../version-25.1/platform-enterprise.md | 2 +- .../version-25.1/reports/overview.md | 8 ++++---- .../version-25.1/secrets/overview.md | 4 ++-- .../supported_software/dragen/overview.md | 2 +- .../azure_troubleshooting.md | 4 ++-- .../troubleshooting_and_faqs/nextflow.md | 8 ++++---- .../troubleshooting_and_faqs/troubleshooting.md | 2 +- .../version-25.2/compute-envs/aws-batch.md | 8 ++++---- .../version-25.2/compute-envs/azure-batch.md | 10 +++++----- .../compute-envs/google-cloud-batch.md | 8 ++++---- .../version-25.2/compute-envs/hpc.md | 4 ++-- .../version-25.2/compute-envs/overview.md | 4 ++-- .../advanced-topics/manual-azure-batch-setup.md | 6 +++--- .../version-25.2/enterprise/configuration/wave.md | 2 +- .../getting-started/deployment-options.md | 2 +- .../version-25.2/getting-started/proteinfold.md | 2 +- .../quickstart-demo/launch-pipelines.md | 2 +- .../version-25.2/getting-started/rnaseq.md | 2 +- .../version-25.2/launch/advanced.md | 4 ++-- .../version-25.2/launch/cache-resume.mdx | 8 ++++---- .../version-25.2/launch/launchpad.md | 6 +++--- .../version-25.2/monitoring/overview.md | 2 +- .../version-25.2/platform-enterprise.md | 2 +- .../version-25.2/reports/overview.md | 8 ++++---- .../version-25.2/secrets/overview.md | 4 ++-- .../supported_software/dragen/overview.md | 2 +- .../azure_troubleshooting.md | 4 ++-- .../troubleshooting_and_faqs/nextflow.md | 8 ++++---- .../troubleshooting_and_faqs/troubleshooting.md | 2 +- .../version-25.3/compute-envs/aws-batch.md | 8 ++++---- .../version-25.3/compute-envs/azure-batch.md | 10 +++++----- .../compute-envs/google-cloud-batch.md | 8 ++++---- .../version-25.3/compute-envs/hpc.md | 4 ++-- .../version-25.3/compute-envs/overview.md | 4 ++-- .../credentials/aws_registry_credentials.md | 2 +- .../credentials/azure_registry_credentials.md | 2 +- .../credentials/docker_hub_registry_credentials.md | 2 +- .../credentials/gitea_registry_credentials.md | 2 +- .../credentials/github_registry_credentials.md | 2 +- .../credentials/gitlab_registry_credentials.md | 2 +- .../credentials/google_registry_credentials.md | 2 +- .../credentials/quay_registry_credentials.md | 2 +- .../advanced-topics/manual-azure-batch-setup.md | 6 +++--- .../version-25.3/enterprise/configuration/wave.md | 2 +- .../getting-started/deployment-options.md | 2 +- .../version-25.3/getting-started/proteinfold.md | 2 +- .../quickstart-demo/launch-pipelines.md | 2 +- .../version-25.3/getting-started/rnaseq.md | 2 +- .../version-25.3/launch/advanced.md | 4 ++-- .../version-25.3/launch/cache-resume.mdx | 8 ++++---- .../version-25.3/launch/launchpad.md | 6 +++--- .../version-25.3/monitoring/overview.md | 2 +- .../version-25.3/pipelines/overview.md | 2 +- .../version-25.3/platform-enterprise.md | 2 +- .../version-25.3/reports/overview.md | 8 ++++---- .../version-25.3/secrets/overview.md | 4 ++-- .../supported_software/dragen/overview.md | 2 +- .../azure_troubleshooting.md | 4 ++-- .../troubleshooting_and_faqs/nextflow.md | 8 ++++---- .../troubleshooting_and_faqs/troubleshooting.md | 2 +- 340 files changed, 637 insertions(+), 637 deletions(-) diff --git a/changelog/seqera-enterprise/v22.3.md b/changelog/seqera-enterprise/v22.3.md index eb66cf112..38d889087 100644 --- a/changelog/seqera-enterprise/v22.3.md +++ b/changelog/seqera-enterprise/v22.3.md @@ -47,7 +47,7 @@ This feature is currently only available on Tower Cloud (tower.nf). For more inf ### Wave containers (technology preview) -Tower now supports the Nextflow [Wave](https://www.nextflow.io/docs/latest/wave.html) container provisioning and augmentation service. When a pipeline is run in Nextflow using Wave, the Wave service uses a Dockerfile stored in the process directory to build a container in the target registry. When the container to be used for process execution is returned, the Wave service can add functional layers and data on-the-fly before it is returned to Nextflow for actual process execution. +Tower now supports the Nextflow [Wave](https://docs.seqera.io/nextflow/wave) container provisioning and augmentation service. When a pipeline is run in Nextflow using Wave, the Wave service uses a Dockerfile stored in the process directory to build a container in the target registry. When the container to be used for process execution is returned, the Wave service can add functional layers and data on-the-fly before it is returned to Nextflow for actual process execution. Wave also enables the use of private container registries in Nextflow — [registry credentials](https://docs.seqera.io/platform-cloud/credentials/overview) stored in Tower are used to authenticate to private container registries with the Wave service. diff --git a/changelog/seqera-enterprise/v22.4.md b/changelog/seqera-enterprise/v22.4.md index 9904bdf07..8d34c92b4 100644 --- a/changelog/seqera-enterprise/v22.4.md +++ b/changelog/seqera-enterprise/v22.4.md @@ -33,7 +33,7 @@ The **All runs** view is accessible via the user menu. ### Wave support for Tower Enterprise -All Tower instances with internet access can now connect to the Seqera Labs Wave container service to leverage its container augmentation and Fusion v2 file system capabilities. See the [Wave containers documentation](https://www.nextflow.io/docs/latest/wave.html) for more information about Wave containers. +All Tower instances with internet access can now connect to the Seqera Labs Wave container service to leverage its container augmentation and Fusion v2 file system capabilities. See the [Wave containers documentation](https://docs.seqera.io/nextflow/wave) for more information about Wave containers. The Wave integration also allows for the secure transfer of credentials required to access private registries between services. See the [Tower documentation](https://docs.seqera.io/platform-enterprise/23.3) to learn how to use the feature in your enterprise installation. diff --git a/changelog/seqera-enterprise/v23.4.md b/changelog/seqera-enterprise/v23.4.md index c0651640d..441bae53c 100644 --- a/changelog/seqera-enterprise/v23.4.md +++ b/changelog/seqera-enterprise/v23.4.md @@ -62,7 +62,7 @@ The Docker Compose CLI plugin replaces the standalone `docker-compose` binary, w **Cloud compute environments use cloud cache by default** -When a cloud storage location is provided as the pipeline work directory in a cloud compute environment, a scratch folder is created in that location to be used for the Nextflow process cache by default. This can be overridden with an alternate cache entry in your [Nextflow configuration](https://www.nextflow.io/docs/latest/process.html#process-cache). +When a cloud storage location is provided as the pipeline work directory in a cloud compute environment, a scratch folder is created in that location to be used for the Nextflow process cache by default. This can be overridden with an alternate cache entry in your [Nextflow configuration](https://docs.seqera.io/nextflow/process). **Login redirection logic update** diff --git a/changelog/seqera-enterprise/v25.1.md b/changelog/seqera-enterprise/v25.1.md index 5306a1b4a..0f1261e3b 100644 --- a/changelog/seqera-enterprise/v25.1.md +++ b/changelog/seqera-enterprise/v25.1.md @@ -105,7 +105,7 @@ Seqera Platform 25.1 includes Nextflow 24.10.5 (previously 24.10.4 from v24.2). According to the [24.10.0](https://github.com/nextflow-io/nextflow/releases/tag/v24.10.0) through [24.10.5](https://github.com/nextflow-io/nextflow/releases/tag/v24.10.5) release notes, this update includes improvements and bug fixes. Existing pipelines will continue to work. -See the [Nextflow 24.10 migration guide](https://www.nextflow.io/docs/latest/migrations/24-10.html) for full details. +See the [Nextflow 24.10 migration guide](https://docs.seqera.io/nextflow/migrations/24-10) for full details. :::note The default Nextflow version can be overridden by setting `NXF_VER` in a [pre-run script](https://docs.seqera.io/platform-enterprise/25.1/launch/advanced#pre-and-post-run-scripts): diff --git a/changelog/seqera-enterprise/v25.2.md b/changelog/seqera-enterprise/v25.2.md index 0c43317d0..2c66e5b1f 100644 --- a/changelog/seqera-enterprise/v25.2.md +++ b/changelog/seqera-enterprise/v25.2.md @@ -41,7 +41,7 @@ Single instance compute environments create a single compute instance to execute ### Fusion - Added Fusion Snapshots (beta) support in AWS Batch compute environments, enabling Fusion to automatically restore jobs interrupted by AWS Spot instance reclamation. See [Fusion Snapshots](https://docs.seqera.io/fusion/guide/snapshots) for more information. -- Fusion licensing enabled. A Fusion license sets a specific quota for Fusion use, measured by total pipeline throughput per month (defined by [Nextflow's I/O metrics](https://www.nextflow.io/docs/latest/tutorials/metrics.html#i-o-usage)). See [Fusion licensing](https://docs.seqera.io/fusion/licensing) for more information. +- Fusion licensing enabled. A Fusion license sets a specific quota for Fusion use, measured by total pipeline throughput per month (defined by [Nextflow's I/O metrics](https://docs.seqera.io/nextflow/tutorials/metrics#i-o-usage)). See [Fusion licensing](https://docs.seqera.io/fusion/licensing) for more information. - Added a Platform Fusion usage dashboard. ### Audit logs @@ -153,7 +153,7 @@ According to the [25.04.0](https://github.com/nextflow-io/nextflow/releases/tag/ - AWS Java SDK upgraded from v1 to v2 (affects `aws.client` config options) - Package `nextflow.config.schema` renamed to `nextflow.config.spec` -See the [Nextflow 25.04 migration guide](https://www.nextflow.io/docs/latest/migrations/25-04.html) for full details. +See the [Nextflow 25.04 migration guide](https://docs.seqera.io/nextflow/migrations/25-04) for full details. :::note The default Nextflow version can be overridden by setting `NXF_VER` in a [pre-run script](https://docs.seqera.io/platform-enterprise/25.2/launch/advanced#pre-and-post-run-scripts): @@ -175,7 +175,7 @@ If you're using AWS Batch, you will need to configure a custom job-definition an ### Removed `maxSpotattempts` setting from Platform -Nextflow now handles this setting. See the [Nextflow reference documentation](https://www.nextflow.io/docs/latest/reference/config.html) for more information. +Nextflow now handles this setting. See the [Nextflow reference documentation](https://docs.seqera.io/nextflow/reference/config) for more information. ### Legacy Seqera container image registry access ended June 1, 2025 diff --git a/changelog/seqera-enterprise/v25.3.1.md b/changelog/seqera-enterprise/v25.3.1.md index c5842e943..7ad4288bf 100644 --- a/changelog/seqera-enterprise/v25.3.1.md +++ b/changelog/seqera-enterprise/v25.3.1.md @@ -35,7 +35,7 @@ According to the [25.10.0](https://github.com/nextflow-io/nextflow/releases/tag/ - AWS Java SDK upgraded from v1 to v2 (affects `aws.client` config options) - Package `nextflow.config.schema` renamed to `nextflow.config.spec` -See the [Nextflow 25.10 migration guide](https://www.nextflow.io/docs/latest/migrations/25-10.html) for full details. +See the [Nextflow 25.10 migration guide](https://docs.seqera.io/nextflow/migrations/25-10) for full details. **Note:** The default Nextflow version can be overridden by setting `NXF_VER` in a [pre-run script](https://docs.seqera.io/platform-enterprise/25.3/launch/advanced#pre-and-post-run-scripts): ```bash diff --git a/changelog/seqera-enterprise/v25.3.md b/changelog/seqera-enterprise/v25.3.md index 4b5cb12e2..d42d0947d 100644 --- a/changelog/seqera-enterprise/v25.3.md +++ b/changelog/seqera-enterprise/v25.3.md @@ -119,7 +119,7 @@ Seqera Platform 25.3 includes Nextflow 25.04.8 (previously 25.04.3 from v25.2). According to the [25.04.0](https://github.com/nextflow-io/nextflow/releases/tag/v25.04.0) through [25.04.8](https://github.com/nextflow-io/nextflow/releases/tag/v25.04.8) release notes, this update includes bug fixes and stability improvements. Existing pipelines will continue to work. -See the [Nextflow 25.04 migration guide](https://www.nextflow.io/docs/latest/migrations/25-04.html) for full details. +See the [Nextflow 25.04 migration guide](https://docs.seqera.io/nextflow/migrations/25-04) for full details. **Note:** The default Nextflow version can be overridden by setting `NXF_VER` in a [pre-run script](https://docs.seqera.io/platform-enterprise/launch/advanced#pre-and-post-run-scripts): ```bash diff --git a/docusaurus.config.js b/docusaurus.config.js index ef6c7c735..875230f7f 100644 --- a/docusaurus.config.js +++ b/docusaurus.config.js @@ -294,7 +294,7 @@ export default async function createConfigAsync() { protocol: 'https', }, ], - apiKey: process.env.TYPESENSE_SEARCH_API_KEY, + apiKey: 'UUIEzlGORRp9lV5GndPR1zYBVBCPIJOl', connectionTimeoutSeconds: 2, }, typesenseSearchParameters: { diff --git a/fusion_docs/guide/aws-eks.md b/fusion_docs/guide/aws-eks.md index fb83960e7..338e05130 100644 --- a/fusion_docs/guide/aws-eks.md +++ b/fusion_docs/guide/aws-eks.md @@ -165,4 +165,4 @@ To use Fusion without the need for escalating privileges, install the Nextflow [ fusion.privileged = false ``` -To use a custom FUSE device plugin, specify it via the `k8s.fuseDevicePlugin` configuration option. See [Kubernetes](https://www.nextflow.io/docs/latest/reference/config.html#k8s) configuration options for details. +To use a custom FUSE device plugin, specify it via the `k8s.fuseDevicePlugin` configuration option. See [Kubernetes](https://docs.seqera.io/nextflow/reference/config#k8s) configuration options for details. diff --git a/fusion_docs/guide/gcp-batch.md b/fusion_docs/guide/gcp-batch.md index c9877d694..c02c7222c 100644 --- a/fusion_docs/guide/gcp-batch.md +++ b/fusion_docs/guide/gcp-batch.md @@ -31,7 +31,7 @@ When Fusion v2 is enabled, the following virtual machine settings are applied: ::: 1. Provide your Google credentials via the `GOOGLE_APPLICATION_CREDENTIALS` environment variable -or with the `gcloud` auth application-default login command. See [Credentials](https://www.nextflow.io/docs/latest/google.html#credentials) for more information. +or with the `gcloud` auth application-default login command. See [Credentials](https://docs.seqera.io/nextflow/google#credentials) for more information. 1. Add the following to your `nextflow.config` file: diff --git a/fusion_docs/guide/gcp-gke.md b/fusion_docs/guide/gcp-gke.md index 85468dab1..5227ac1c6 100644 --- a/fusion_docs/guide/gcp-gke.md +++ b/fusion_docs/guide/gcp-gke.md @@ -117,4 +117,4 @@ To use Fusion without the need for escalating privileges, install the Nextflow [ fusion.privileged = false ``` -To use a custom FUSE device plugin, specify it via the `k8s.fuseDevicePlugin` configuration option. See [Kubernetes](https://www.nextflow.io/docs/latest/reference/config.html#k8s) configuration options for details. +To use a custom FUSE device plugin, specify it via the `k8s.fuseDevicePlugin` configuration option. See [Kubernetes](https://docs.seqera.io/nextflow/reference/config#k8s) configuration options for details. diff --git a/fusion_docs/guide/local/aws-s3.md b/fusion_docs/guide/local/aws-s3.md index b476521ae..3fb5ddc3b 100644 --- a/fusion_docs/guide/local/aws-s3.md +++ b/fusion_docs/guide/local/aws-s3.md @@ -15,7 +15,7 @@ a large storage volume for temporary pipeline data. This configuration requires Docker or a similar container engine to run pipeline tasks. ::: -1. Set `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY` environment variables to grant Nextflow and Fusion access to your storage credentials. See [Credentials](https://www.nextflow.io/docs/latest/google.html#credentials) for more information. +1. Set `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY` environment variables to grant Nextflow and Fusion access to your storage credentials. See [Credentials](https://docs.seqera.io/nextflow/google#credentials) for more information. 1. Add the following to your `nextflow.config` file: diff --git a/fusion_docs/guide/local/azure-blob.md b/fusion_docs/guide/local/azure-blob.md index 3ce8f0c60..4ade6b774 100644 --- a/fusion_docs/guide/local/azure-blob.md +++ b/fusion_docs/guide/local/azure-blob.md @@ -15,7 +15,7 @@ a large storage volume for temporary pipeline data. This configuration requires Docker or a similar container engine to run pipeline tasks. ::: -1. Set `AZURE_STORAGE_ACCOUNT_NAME` and `AZURE_STORAGE_ACCOUNT_KEY` or `AZURE_STORAGE_SAS_TOKEN` environment variables to grant Nextflow and Fusion access to your storage credentials. See [Credentials](https://www.nextflow.io/docs/latest/google.html#credentials) for more information. +1. Set `AZURE_STORAGE_ACCOUNT_NAME` and `AZURE_STORAGE_ACCOUNT_KEY` or `AZURE_STORAGE_SAS_TOKEN` environment variables to grant Nextflow and Fusion access to your storage credentials. See [Credentials](https://docs.seqera.io/nextflow/google#credentials) for more information. 1. Add the following to your `nextflow.config` file: diff --git a/fusion_docs/guide/local/google-cloud.md b/fusion_docs/guide/local/google-cloud.md index 1f977b3b8..6b25f9f06 100644 --- a/fusion_docs/guide/local/google-cloud.md +++ b/fusion_docs/guide/local/google-cloud.md @@ -15,7 +15,7 @@ a large storage volume for temporary pipeline data. This configuration requires Docker or a similar container engine to run pipeline tasks. ::: -1. Set the `GOOGLE_APPLICATION_CREDENTIALS` environment variable with your service account JSON key to grant Nextflow and Fusion access to your storage credentials. See [Credentials](https://www.nextflow.io/docs/latest/google.html#credentials) for more information. +1. Set the `GOOGLE_APPLICATION_CREDENTIALS` environment variable with your service account JSON key to grant Nextflow and Fusion access to your storage credentials. See [Credentials](https://docs.seqera.io/nextflow/google#credentials) for more information. 1. Add the following to your `nextflow.config` file: diff --git a/fusion_docs/guide/local/minio.md b/fusion_docs/guide/local/minio.md index 6083d2fbe..52a0e52ae 100644 --- a/fusion_docs/guide/local/minio.md +++ b/fusion_docs/guide/local/minio.md @@ -31,7 +31,7 @@ This configuration requires Docker or a similar container engine to run pipeline 1. Create storage credentials and a bucket. -1. Set `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY` environment variables to grant Nextflow and Fusion access to your storage credentials. See [Credentials](https://www.nextflow.io/docs/latest/google.html#credentials) for more information. +1. Set `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY` environment variables to grant Nextflow and Fusion access to your storage credentials. See [Credentials](https://docs.seqera.io/nextflow/google#credentials) for more information. 1. Add the following to your `nextflow.config` file: diff --git a/fusion_docs/guide/snapshots/configuration.md b/fusion_docs/guide/snapshots/configuration.md index 322f7b67a..ae17ae512 100644 --- a/fusion_docs/guide/snapshots/configuration.md +++ b/fusion_docs/guide/snapshots/configuration.md @@ -57,9 +57,9 @@ To disable automatic retries, set `maxSpotAttempts = 0`: ### Fine-grained retries with `errorStrategy` -For fine-grained control of retries, configure your Nextflow [`errorStrategy`](https://www.nextflow.io/docs/latest/reference/process.html#errorstrategy) to implement retry logic based on specific checkpoint failure types. This allows you to handle different failure scenarios (e.g., checkpoint dump failures differently from restore failures) differently. +For fine-grained control of retries, configure your Nextflow [`errorStrategy`](https://docs.seqera.io/nextflow/reference/process#errorstrategy) to implement retry logic based on specific checkpoint failure types. This allows you to handle different failure scenarios (e.g., checkpoint dump failures differently from restore failures) differently. -To configure, set to `maxSpotAttempts = 0` and add an [`errorStrategy`](https://www.nextflow.io/docs/latest/reference/process.html#errorstrategy) to your process configuration. For example: +To configure, set to `maxSpotAttempts = 0` and add an [`errorStrategy`](https://docs.seqera.io/nextflow/reference/process#errorstrategy) to your process configuration. For example: ```groovy process { @@ -81,7 +81,7 @@ process { **Configuration options**: -See [`errorStrategy`](https://www.nextflow.io/docs/latest/reference/process.html#errorstrategy) for more configuration options. +See [`errorStrategy`](https://docs.seqera.io/nextflow/reference/process#errorstrategy) for more configuration options. ## TCP connection handling @@ -133,4 +133,4 @@ process.resourceLimits = [cpus: 32, memory: '60.GB'] process.resourceLimits = [cpus: 16, memory: '20.GB'] ``` -See [AWS Batch](./aws.md) or [Google Cloud Batch](./gcp.md) for more information about reclamation windows. See [`resourceLimits`](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits) for more configuration options. +See [AWS Batch](./aws.md) or [Google Cloud Batch](./gcp.md) for more information about reclamation windows. See [`resourceLimits`](https://docs.seqera.io/nextflow/reference/process#resourcelimits) for more configuration options. diff --git a/fusion_docs/licensing.md b/fusion_docs/licensing.md index fafad479f..1e38ad407 100644 --- a/fusion_docs/licensing.md +++ b/fusion_docs/licensing.md @@ -9,7 +9,7 @@ tags: [fusion, storage, compute, file system, license, quotas] Fusion licensing requirements and free tier quotas will be enforced starting June 30th, 2025. [Contact Seqera](https://seqera.io/contact-us) with any questions or licensing requests. ::: -A Fusion license sets a specific quota for Fusion use, measured by total pipeline throughput per month (defined by [Nextflow’s I/O metrics](https://www.nextflow.io/docs/latest/tutorials/metrics.html#i-o-usage)). +A Fusion license sets a specific quota for Fusion use, measured by total pipeline throughput per month (defined by [Nextflow’s I/O metrics](https://docs.seqera.io/nextflow/tutorials/metrics#i-o-usage)). ### For Seqera Cloud @@ -24,5 +24,5 @@ A Fusion license sets a specific quota for Fusion use, measured by total pipelin ### For Seqera Enterprise instances without network connectivity, and direct Fusion use with Nextflow -- Run Fusion using the [`TOWER_ACCESS_TOKEN` environment variable](https://www.nextflow.io/docs/latest/reference/config.html#tower) to allow Nextflow to connect to Seqera Cloud. +- Run Fusion using the [`TOWER_ACCESS_TOKEN` environment variable](https://docs.seqera.io/nextflow/reference/config#tower) to allow Nextflow to connect to Seqera Cloud. - Throughput counts towards the free or paid usage associated with your Cloud organization. diff --git a/fusion_docs/reference.md b/fusion_docs/reference.md index 0aa095370..1c770e528 100644 --- a/fusion_docs/reference.md +++ b/fusion_docs/reference.md @@ -25,5 +25,5 @@ The following options are available: | `fusion.tags` | Tag pattern for files created via the Fusion client. When false, disables file tagging. Default: `[.command.*\|.exitcode\|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)`. | :::note -See [Configuration options](https://www.nextflow.io/docs/latest/reference/config.html#configuration-options) for a full list of Nextflow configuration options. +See [Configuration options](https://docs.seqera.io/nextflow/reference/config#configuration-options) for a full list of Nextflow configuration options. ::: diff --git a/platform-cli-docs/docs/reference/pipelines.md b/platform-cli-docs/docs/reference/pipelines.md index 32bb7d51f..c0b7e4976 100644 --- a/platform-cli-docs/docs/reference/pipelines.md +++ b/platform-cli-docs/docs/reference/pipelines.md @@ -110,7 +110,7 @@ The optional `--params-file` flag is used to pass a set of default parameters th The optional `--config` flag is used to pass a custom Nextflow configuration file — configuration values passed here override the same values in the default pipeline repository `nextflow.conf` file. When this flag is set, all configuration values specified in Platform pipeline or compute environment **Nextflow config** fields are ignored. :::tip -The `params-file` or `--config` file must be a YAML or JSON file using [Nextflow configuration](https://www.nextflow.io/docs/latest/config.html#config-syntax) syntax. +The `params-file` or `--config` file must be a YAML or JSON file using [Nextflow configuration](https://docs.seqera.io/nextflow/config#config-syntax) syntax. ::: ## tw pipelines view diff --git a/platform-cli-docs/docs/reference/runs.md b/platform-cli-docs/docs/reference/runs.md index 7f8ee6b65..5da76efa7 100644 --- a/platform-cli-docs/docs/reference/runs.md +++ b/platform-cli-docs/docs/reference/runs.md @@ -14,7 +14,7 @@ Runs display all the current and previous pipeline runs in the specified workspa - `submitted`: Pending execution - `running`: Running - `succeeded`: Completed successfully -- `failed`: Successfully executed, where at least one task failed with a terminate [error strategy](https://www.nextflow.io/docs/latest/process.html#errorstrategy) +- `failed`: Successfully executed, where at least one task failed with a terminate [error strategy](https://docs.seqera.io/nextflow/process#errorstrategy) - `cancelled`: Stopped manually during execution - `unknown`: Indeterminate status diff --git a/platform-cli-docs/overlays/tw-runs.md b/platform-cli-docs/overlays/tw-runs.md index ace3a76cf..164899168 100644 --- a/platform-cli-docs/overlays/tw-runs.md +++ b/platform-cli-docs/overlays/tw-runs.md @@ -5,6 +5,6 @@ Runs display all the current and previous pipeline runs in the specified workspa - `submitted`: Pending execution - `running`: Running - `succeeded`: Completed successfully -- `failed`: Successfully executed, where at least one task failed with a terminate [error strategy](https://www.nextflow.io/docs/latest/process.html#errorstrategy) +- `failed`: Successfully executed, where at least one task failed with a terminate [error strategy](https://docs.seqera.io/nextflow/process#errorstrategy) - `cancelled`: Stopped manually during execution - `unknown`: Indeterminate status diff --git a/platform-cli-docs/overlays/tw-secrets-add.md b/platform-cli-docs/overlays/tw-secrets-add.md index 0017f4160..68730e97b 100644 --- a/platform-cli-docs/overlays/tw-secrets-add.md +++ b/platform-cli-docs/overlays/tw-secrets-add.md @@ -4,7 +4,7 @@ Run `tw secrets add -h` to view the required and optional fields for adding a se [compute-envs]: /platform-cloud/compute-envs/overview [credentials]: /platform-cloud/credentials/overview [git-integration]: /platform-cloud/git/overview -[nextflow-config]: https://www.nextflow.io/docs/latest/config.html#config-syntax +[nextflow-config]: https://docs.seqera.io/nextflow/config#config-syntax [participant-roles]: /platform-cloud/orgs-and-teams/roles [shared-workspaces]: /platform-cloud/orgs-and-teams/workspace-management [tower-agent]: /platform-cloud/supported_software/agent/overview diff --git a/platform-cloud/docs/compute-envs/aws-batch.md b/platform-cloud/docs/compute-envs/aws-batch.md index 57f04a7f0..9c7a65dc0 100644 --- a/platform-cloud/docs/compute-envs/aws-batch.md +++ b/platform-cloud/docs/compute-envs/aws-batch.md @@ -688,7 +688,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM 1. In the **Pipeline work directory** field type or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation), e.g., `s3://seqera-bucket`. The work directory can be customized to specify a folder inside the bucket where Nextflow intermediate files will be stored, e.g., `s3://seqera-bucket/nextflow-workdir`. The bucket must be located in the same region chosen in the previous step. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -697,7 +697,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM Using an EFS or FSx file system as your work directory is currently incompatible with [Studios](../studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
@@ -920,7 +920,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See 1. Select a **Region**, e.g., _eu-west-1 - Europe (Ireland)_. This region must match the region where your S3 bucket or EFS/FSx work directory is located to avoid high data transfer costs. 1. Enter or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation) in the **Pipeline work directory** field, e.g., `s3://seqera-bucket`. This bucket must be in the same region chosen in the previous step to avoid incurring high data transfer costs. The work directory can be customized to specify a folder inside the bucket, e.g., `s3://seqera-bucket/nextflow-workdir`. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -929,7 +929,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See Using an EFS or FSx file system as your work directory is currently incompatible with [Studios](../studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
diff --git a/platform-cloud/docs/compute-envs/azure-batch.md b/platform-cloud/docs/compute-envs/azure-batch.md index 1b79b5c87..f9283002b 100644 --- a/platform-cloud/docs/compute-envs/azure-batch.md +++ b/platform-cloud/docs/compute-envs/azure-batch.md @@ -189,7 +189,7 @@ Nextflow can authenticate to Azure services using a managed identity. This metho When you use a manually-configured compute environment with a managed identity attached to the Azure Batch Pool, Nextflow can use this managed identity for authentication. However, Seqera still needs to use access keys or an Entra service principal to submit the initial task to Azure Batch to run Nextflow, which will then proceed with the managed identity for subsequent authentication. 1. In Azure, create a user-assigned managed identity. See [Manage user-assigned managed identities](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-manage-user-assigned-managed-identities) for detailed steps. Take note of the client ID of the managed identity when you create it. -1. The user-assigned managed identity must have the necessary access roles for Nextflow. See [Required role assignments](https://www.nextflow.io/docs/latest/azure.html#required-role-assignments) for more information. +1. The user-assigned managed identity must have the necessary access roles for Nextflow. See [Required role assignments](https://docs.seqera.io/nextflow/azure#required-role-assignments) for more information. 1. Associate the user-assigned managed identity with the Azure Batch Pool. See [Set up managed identity in your Batch pool](https://learn.microsoft.com/en-us/troubleshoot/azure/hpc/batch/use-managed-identities-azure-batch-account-pool#set-up-managed-identity-in-your-batch-pool) for more information. 1. When you set up the Seqera compute environment, select the Azure Batch pool by name and enter the managed identity client ID in the specified field as instructed above. @@ -252,7 +252,7 @@ Create a Batch Forge Azure Batch compute environment: 1. Select a **Region**, such as _eastus_. 1. In the **Work directory** field, enter the Azure blob container created previously. For example, `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. 1. Select **Enable Fusion v2** to allow access to your Azure Blob Storage data via the [Fusion v2][fusion-docs] virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. @@ -285,7 +285,7 @@ Create a Batch Forge Azure Batch compute environment: 1. Enter the **VMs count**. If autoscaling is enabled (default), this is the maximum number of VMs you wish the pool to scale up to. If autoscaling is disabled, this is the fixed number of virtual machines in the pool. 1. Enable **Autoscale** to scale up and down automatically, based on the number of pipeline tasks. The number of VMs will vary from **0** to **VMs count**. 1. Enable **Dispose resources** for Seqera to automatically delete the Batch pool if the compute environment is deleted on the platform. -1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://www.nextflow.io/docs/latest/wave.html) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. +1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://docs.seqera.io/nextflow/wave) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. 1. Apply [**Resource labels**](../resource-labels/overview). This will populate the **Metadata** fields of the Azure Batch pool. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. @@ -396,7 +396,7 @@ The following settings can be modified after creating a pool: 1. Select a **Region**, such as _eastus (East US)_. 1. In the **Work directory** field, add the Azure blob container created previously. For example, `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. 1. Select **Enable Fusion v2** to allow access to your Azure Blob Storage data via the [Fusion v2][fusion-docs] virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. @@ -463,7 +463,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [az-vm-gen]: https://learn.microsoft.com/en-us/azure/virtual-machines/generation-2 [az-disk-type]: https://learn.microsoft.com/en-us/azure/virtual-machines/disks-types [az-batch-autoscale]: https://learn.microsoft.com/en-us/azure/batch/batch-automatic-scaling -[az-file-shares]: https://www.nextflow.io/docs/latest/azure.html#azure-file-shares +[az-file-shares]: https://docs.seqera.io/nextflow/azure#azure-file-shares [az-vm-sizes]: https://learn.microsoft.com/en-us/azure/virtual-machines/sizes/overview [wave-docs]: https://docs.seqera.io/wave diff --git a/platform-cloud/docs/compute-envs/google-cloud-batch.md b/platform-cloud/docs/compute-envs/google-cloud-batch.md index 04f7217fb..be8cf205e 100644 --- a/platform-cloud/docs/compute-envs/google-cloud-batch.md +++ b/platform-cloud/docs/compute-envs/google-cloud-batch.md @@ -148,7 +148,7 @@ Select the **Location** where you will execute your pipelines. See [Location][lo In the **Work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the location selected in the previous step. :::note -When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. +When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: #### Seqera features @@ -172,7 +172,7 @@ Select **Enable Fusion v2** to allow access to your Google Cloud Storage data vi :::note To specify virtual machine settings in Platform during compute environment creation, use the **Global Nextflow config** field to apply custom Nextflow process directives to all pipeline runs launched with this compute environment. - To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://www.nextflow.io/docs/latest/google.html#process-definition) for more information. + To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://docs.seqera.io/nextflow/google#process-definition) for more information. ::: When Fusion v2 is enabled, the following virtual machine settings are applied: @@ -232,7 +232,7 @@ If you use VM instance templates for the head or compute jobs (see step 6 below) :::caution Seqera does not validate the VM instance template you specify in these fields. Generally, use templates that define only the machine type, network, disk, and configuration values that will not change across multiple VM instances and Seqera compute environments. See [Create instance templates](https://cloud.google.com/compute/docs/instance-templates/create-instance-templates) for instructions to create your instance templates. - To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://www.nextflow.io/docs/latest/google.html#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://www.nextflow.io/docs/latest/config.html#config-process-selectors) to assign separate templates to each of your processes. + To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://docs.seqera.io/nextflow/google#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://docs.seqera.io/nextflow/config#config-process-selectors) to assign separate templates to each of your processes. ::: Select **Create** to finalize the compute environment setup. @@ -245,7 +245,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [create-sa]: https://cloud.google.com/iam/docs/service-accounts-create#creating [get-json]: https://cloud.google.com/iam/docs/keys-list-get#get-key [location]: https://cloud.google.com/compute/docs/regions-zones#available -[wave-docs]: https://www.nextflow.io/docs/latest/wave.html +[wave-docs]: https://docs.seqera.io/nextflow/wave [fusion-docs]: https://docs.seqera.io/fusion [platform-fusion-docs]: ../supported_software/fusion/overview [pre-post-run-scripts]: ../launch/advanced#pre-and-post-run-scripts diff --git a/platform-cloud/docs/compute-envs/hpc.md b/platform-cloud/docs/compute-envs/hpc.md index ed65646d1..c69182557 100644 --- a/platform-cloud/docs/compute-envs/hpc.md +++ b/platform-cloud/docs/compute-envs/hpc.md @@ -19,13 +19,13 @@ To launch pipelines into an **HPC** cluster from Seqera, the following requireme - The cluster should allow outbound connections to the Seqera web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Credentials -Seqera requires SSH access to your HPC cluster to run pipelines. Use [managed identities](../credentials/managed_identities) to enable granular access control and preserve individual cluster user identities. +Seqera requires SSH access to your HPC cluster to run pipelines. Use [managed identities](../credentials/managed_identities) to enable granular access control and preserve individual cluster user identities. -You can also use workspace [SSH credentials](../credentials/ssh_credentials) for cluster login, but this provides service account access to your HPC to all Platform users. This means that all users will be granted the same file system access, and all activity is logged under the same user account on your HPC cluster. +You can also use workspace [SSH credentials](../credentials/ssh_credentials) for cluster login, but this provides service account access to your HPC to all Platform users. This means that all users will be granted the same file system access, and all activity is logged under the same user account on your HPC cluster. For HPC clusters that do not allow direct access through an SSH client, a secure connection can be authenticated with [Tower Agent](../supported_software/agent/overview). @@ -64,13 +64,13 @@ To create a new **HPC** compute environment: 1. Enter the absolute path of the **Launch directory** to be used on the cluster. If omitted, it will be the same as the work directory. 1. Enter the **Login hostname**. This is usually the hostname or public IP address of the cluster's login node. -1. Enter the **Head queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will be submitted. -1. Enter the **Compute queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will submit tasks. +1. Enter the **Head queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will be submitted. +1. Enter the **Compute queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will submit tasks. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. - - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. + - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. :::info - Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced#nextflow-config-file) for more information on configuration priority. + Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced#nextflow-config-file) for more information on configuration priority. ::: 1. Specify custom **Environment variables** for the head job and/or compute jobs. 1. Configure any advanced options needed: diff --git a/platform-cloud/docs/compute-envs/overview.md b/platform-cloud/docs/compute-envs/overview.md index 5ccb29a56..719f3858c 100644 --- a/platform-cloud/docs/compute-envs/overview.md +++ b/platform-cloud/docs/compute-envs/overview.md @@ -64,8 +64,8 @@ Some important considerations: - Seqera only supports NVIDIA GPUs. Select instances with NVIDIA GPUs for your GPU-dependent processes. - The **Enable GPUs** setting causes Batch Forge to specify the most current [AWS-recommended GPU-optimized ECS AMI](https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ecs-optimized_AMI.html) as the EC2 fleet AMI when creating the compute environment. This setting can be overridden by **AMI ID** in the advanced options. - The **Enable GPUs** setting alone does not deploy GPU instances in your compute environment. You must still specify GPU-enabled instance types in the **Advanced options > Instance types** field. -- Your Nextflow script must include [accelerator directives](https://www.nextflow.io/docs/latest/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. -- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: +- Your Nextflow script must include [accelerator directives](https://docs.seqera.io/nextflow/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. +- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://docs.seqera.io/nextflow/process#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: ```groovy process { diff --git a/platform-cloud/docs/enterprise/advanced-topics/manual-azure-batch-setup.md b/platform-cloud/docs/enterprise/advanced-topics/manual-azure-batch-setup.md index 2172185aa..6a234a4e2 100644 --- a/platform-cloud/docs/enterprise/advanced-topics/manual-azure-batch-setup.md +++ b/platform-cloud/docs/enterprise/advanced-topics/manual-azure-batch-setup.md @@ -268,7 +268,7 @@ Select **Launch** next to the `hello-world-autopool` pipeline in your workspace Seqera can utilize an Azure Entra service principal to authenticate and access Azure Batch for job execution and Azure Storage for data management, and Nextflow can authenticate to Azure services using a managed identity. This method offers enhanced security compared to access keys, but must run on Azure infrastructure. -See [Microsoft Entra](https://www.nextflow.io/docs/latest/azure.html#microsoft-entra) in the Nextflow documentation for more information. +See [Microsoft Entra](https://docs.seqera.io/nextflow/azure#microsoft-entra) in the Nextflow documentation for more information. #### Create a service principal for Seqera to use for authentication @@ -288,7 +288,7 @@ In Seqera: Back in the Azure Portal: 1. [Create a managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-manage-user-assigned-managed-identities?pivots=identity-mi-methods-azp) -1. [Assign the relevant roles to the managed identity](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current). See [Required role assignments](https://www.nextflow.io/docs/latest/azure.html#required-role-assignments) for Nextflow requirements. +1. [Assign the relevant roles to the managed identity](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current). See [Required role assignments](https://docs.seqera.io/nextflow/azure#required-role-assignments) for Nextflow requirements. 1. Note the managed identity client ID for later. 1. In the Azure Portal, go to the Batch account you created earlier. 1. Go to the **Pools** tab and find the pool called `tower-pool-${id}`, where `${id}` is the ID of the head node pool created earlier. @@ -429,6 +429,6 @@ If you wish to keep the Azure resources, you can remove each pool within a Batch [install-azure-cli]: https://learn.microsoft.com/en-us/cli/azure/install-azure-cli [install-seqera-cli]: /platform-cli/installation -[nextflow-working-directory]: https://www.nextflow.io/docs/latest/cache-and-resume.html#work-directory +[nextflow-working-directory]: https://docs.seqera.io/nextflow/cache-and-resume#work-directory [create-org-workspace]: ../../getting-started/workspace-setup [add-pipeline]: ../../getting-started/quickstart-demo/add-pipelines#add-from-the-launchpad diff --git a/platform-cloud/docs/getting-started/deployment-options.md b/platform-cloud/docs/getting-started/deployment-options.md index 4bf8c72f8..b30b3b2e2 100644 --- a/platform-cloud/docs/getting-started/deployment-options.md +++ b/platform-cloud/docs/getting-started/deployment-options.md @@ -96,5 +96,5 @@ If you have an existing environment where you run Nextflow directly, you can sti You can now monitor your workflow runs in the Seqera interface. To configure and execute Nextflow pipelines in cloud environments, see [compute environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-cloud/docs/getting-started/proteinfold.md b/platform-cloud/docs/getting-started/proteinfold.md index 3e411ab64..e8f3ff947 100644 --- a/platform-cloud/docs/getting-started/proteinfold.md +++ b/platform-cloud/docs/getting-started/proteinfold.md @@ -183,7 +183,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL: `https://github.com/nf-core/proteinfold`. For saved pipelines, this is prefilled and cannot be edited. - **Revision**: A valid repository commit ID, tag, or branch name: `1.1.1`. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-cloud/docs/getting-started/quickstart-demo/launch-pipelines.md b/platform-cloud/docs/getting-started/quickstart-demo/launch-pipelines.md index ddbc10c08..5615cc7a3 100644 --- a/platform-cloud/docs/getting-started/quickstart-demo/launch-pipelines.md +++ b/platform-cloud/docs/getting-started/quickstart-demo/launch-pipelines.md @@ -49,7 +49,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc :::info See [Git revision management](../../pipelines/revision.md) for more information on **Commit ID**, **Pull latest**, and **Revision** behavior. ::: -- (*Optional*) **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. +- (*Optional*) **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - (*Optional*) **Labels**: Assign new or existing [labels](../../labels/overview) to the run. - **Compute environment**: Select an existing workspace [compute environment](../../compute-envs/overview). diff --git a/platform-cloud/docs/getting-started/rnaseq.md b/platform-cloud/docs/getting-started/rnaseq.md index 523908a1d..b37218347 100644 --- a/platform-cloud/docs/getting-started/rnaseq.md +++ b/platform-cloud/docs/getting-started/rnaseq.md @@ -196,7 +196,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. - **Revision**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-cloud/docs/launch/advanced.md b/platform-cloud/docs/launch/advanced.md index 8df0ac6a3..3c12365b9 100644 --- a/platform-cloud/docs/launch/advanced.md +++ b/platform-cloud/docs/launch/advanced.md @@ -9,7 +9,7 @@ You can modify the configuration and execution of a pipeline with advanced launc ### Nextflow config file -Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://www.nextflow.io/docs/latest/config.html#config-syntax). +Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax). For example, modify the **manifest** section to give the pipeline a name and description that will show up in the Seqera monitoring section: @@ -122,7 +122,7 @@ Post-run script failures do not affect the workflow exit status. Post-run script ### Stub run -Replace Nextflow process commands with command [stubs](https://www.nextflow.io/docs/latest/process.html#stub), where defined, before execution. +Replace Nextflow process commands with command [stubs](https://docs.seqera.io/nextflow/process#stub), where defined, before execution. ### Main script diff --git a/platform-cloud/docs/launch/cache-resume.mdx b/platform-cloud/docs/launch/cache-resume.mdx index 1b571ceb9..1d7869946 100644 --- a/platform-cloud/docs/launch/cache-resume.mdx +++ b/platform-cloud/docs/launch/cache-resume.mdx @@ -8,13 +8,13 @@ tags: [cache, launch, resume, relaunch] import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; -Nextflow maintains a [cache](https://www.nextflow.io/docs/latest/cache-and-resume.html) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. +Nextflow maintains a [cache](https://docs.seqera.io/nextflow/cache-and-resume) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. ## Cache directory -Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. +Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. -To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://www.nextflow.io/docs/latest/process.html#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). +To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://docs.seqera.io/nextflow/process#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). @@ -108,7 +108,7 @@ Kubernetes compute environments do not use cloud cache by default. To specify a Google Cloud Storage 1. See [these instructions](../compute-envs/google-cloud-batch#iam) to set up IAM and create a JSON key file for the custom service account with permissions to your Google Cloud storage account. - 2. If you run the [gcloud CLI authentication flow](https://nextflow.io/docs/edge/google.html#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. + 2. If you run the [gcloud CLI authentication flow](https://docs.seqera.io/nextflow/google#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. 3. Add the following to the **Nextflow Config file** field when you [launch](../launch/launchpad#launch-form) your pipeline: ```groovy diff --git a/platform-cloud/docs/launch/launchpad.md b/platform-cloud/docs/launch/launchpad.md index 7189fe720..0c2310afa 100644 --- a/platform-cloud/docs/launch/launchpad.md +++ b/platform-cloud/docs/launch/launchpad.md @@ -33,7 +33,7 @@ The launch form accepts URL query parameters. See [Populate launch form with URL - **Pipeline to launch**: A Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. Private repositories require [access credentials](../credentials/overview). :::note - Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://www.nextflow.io/docs/latest/sharing.html) in the Nextflow docs for more details. + Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://docs.seqera.io/nextflow/sharing) in the Nextflow docs for more details. ::: - **Revision**: A valid repository commit ID, tag, or branch name. Determines the version of the pipeline to launch. - **Commit ID**: Pin pipeline revision to the most recent HEAD commit ID. If no commit ID is pinned, the latest revision of the repository branch or tag is used. @@ -41,7 +41,7 @@ The launch form accepts URL query parameters. See [Populate launch form with URL :::info See [Git revision management](../pipelines/revision.md) for more information on **Commit ID**, **Pull latest**, and **Revision** behavior. ::: -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: A unique identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: The [compute environment](../compute-envs/overview) where the run will be launched. @@ -116,7 +116,7 @@ Use resource labels to tag the computing resources created during the workflow e Secrets are used to store keys and tokens used by workflow tasks to interact with external systems. Enter the names of any stored user or workspace secrets required for the workflow execution. :::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: #### Advanced options diff --git a/platform-cloud/docs/monitoring/overview.md b/platform-cloud/docs/monitoring/overview.md index 9375531c3..8421b04f8 100644 --- a/platform-cloud/docs/monitoring/overview.md +++ b/platform-cloud/docs/monitoring/overview.md @@ -12,7 +12,7 @@ The **Runs** tab contains all previous runs in the workspace. Each new or resume - `submitted`: Pending execution - `running`: Running - `succeeded`: Completed successfully -- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://www.nextflow.io/docs/latest/process.html#errorstrategy) +- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://docs.seqera.io/nextflow/process#errorstrategy) - `cancelled`: Stopped manually during execution - `unknown`: Indeterminate status diff --git a/platform-cloud/docs/pipelines/overview.md b/platform-cloud/docs/pipelines/overview.md index ae449189d..4118103f6 100644 --- a/platform-cloud/docs/pipelines/overview.md +++ b/platform-cloud/docs/pipelines/overview.md @@ -11,7 +11,7 @@ When you add a pipeline to Seqera, you define: - The pipeline Git repository and [revision](./revision.md) (branch, tag, or commit) - [Compute environment](../compute-envs/overview.md) for execution -- Pipeline parameters and [configuration profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) +- Pipeline parameters and [configuration profiles](https://docs.seqera.io/nextflow/config#config-profiles) - (Optional) [Labels](../labels/overview.md), [resource labels](../resource-labels/overview.md), and [secrets](../secrets/overview.md) - (Optional) [Pre-run and post-run](../launch/advanced.md#pre-and-post-run-scripts) bash scripts that execute in your compute environment diff --git a/platform-cloud/docs/platform-cloud.md b/platform-cloud/docs/platform-cloud.md index 243dd6a2f..42cc47bf8 100644 --- a/platform-cloud/docs/platform-cloud.md +++ b/platform-cloud/docs/platform-cloud.md @@ -37,4 +37,4 @@ Upon your first login, you arrive in `community/showcase`, a workspace pre-fille Nextflow is both a programming workflow language and an execution runtime that supports a wide range of execution platforms, including popular traditional grid scheduling systems such as Slurm and IBM LSF, and cloud services such as AWS, Azure, and Google Cloud Batch. -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/) to learn more. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/) to learn more. diff --git a/platform-cloud/docs/reports/overview.md b/platform-cloud/docs/reports/overview.md index bbb37d89d..a46782505 100644 --- a/platform-cloud/docs/reports/overview.md +++ b/platform-cloud/docs/reports/overview.md @@ -83,10 +83,10 @@ By default, the MIME type is deduced from the file extension, so you don't need Nextflow can generate a number of built-in reports: -- [Execution report](https://nextflow.io/docs/latest/tracing.html#execution-report) -- [Execution timeline](https://nextflow.io/docs/latest/tracing.html#timeline-report) -- [Trace file](https://nextflow.io/docs/latest/tracing.html#trace-report) -- [Workflow diagram](https://nextflow.io/docs/latest/tracing.html#dag-visualisation) (i.e. DAG) +- [Execution report](https://docs.seqera.io/nextflow/tracing#execution-report) +- [Execution timeline](https://docs.seqera.io/nextflow/tracing#timeline-report) +- [Trace file](https://docs.seqera.io/nextflow/tracing#trace-report) +- [Workflow diagram](https://docs.seqera.io/nextflow/tracing#dag-visualisation) (i.e. DAG) In Nextflow version 24.03.0-edge and later, these reports can be included as pipeline reports in Platform. Specify them in `tower.yml` like any other file: diff --git a/platform-cloud/docs/secrets/overview.md b/platform-cloud/docs/secrets/overview.md index adf90cb66..cb4ec764a 100644 --- a/platform-cloud/docs/secrets/overview.md +++ b/platform-cloud/docs/secrets/overview.md @@ -31,12 +31,12 @@ Secrets defined by a user have higher priority and will override any secrets wit ## Use secrets in workflows -When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://www.nextflow.io/docs/edge/secrets.html#process-secrets) for more information. +When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://docs.seqera.io/nextflow/secrets) for more information. Secrets are automatically deleted from the secret manager when the pipeline completes, successfully or unsuccessfully. :::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: ## AWS Secrets Manager integration diff --git a/platform-cloud/docs/supported_software/dragen/overview.md b/platform-cloud/docs/supported_software/dragen/overview.md index 9e7841834..b0d6aa4a8 100644 --- a/platform-cloud/docs/supported_software/dragen/overview.md +++ b/platform-cloud/docs/supported_software/dragen/overview.md @@ -80,7 +80,7 @@ See the [dragen.nf](https://github.com/seqeralabs/nf-dragen/blob/master/modules/ } ``` - See the [Nextflow label docs](https://www.nextflow.io/docs/latest/process.html?highlight=label#label) for more information. + See the [Nextflow label docs](https://docs.seqera.io/nextflow/process.html?highlight=label#label) for more information. 2. Define secrets in Seqera: diff --git a/platform-cloud/docs/troubleshooting_and_faqs/azure_troubleshooting.md b/platform-cloud/docs/troubleshooting_and_faqs/azure_troubleshooting.md index 184271aea..17beb0d70 100644 --- a/platform-cloud/docs/troubleshooting_and_faqs/azure_troubleshooting.md +++ b/platform-cloud/docs/troubleshooting_and_faqs/azure_troubleshooting.md @@ -20,12 +20,12 @@ The default Azure Batch implementation in Seqera Platform uses a single pool for - One [Low priority](https://learn.microsoft.com/en-us/azure/batch/batch-spot-vms#differences-between-spot-and-low-priority-vms) :::note -Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://www.nextflow.io/docs/latest/azure.html#requirements-on-pre-existing-named-pools). +Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://docs.seqera.io/nextflow/azure#requirements-on-pre-existing-named-pools). ::: 2. Create a manual [Azure Batch](../compute-envs/azure-batch#manual) compute environment in Seqera Platform. 3. In **Compute pool name**, specify your dedicated Batch pool. -4. Specify the Low priority pool using the `process.queue` [directive](https://www.nextflow.io/docs/latest/process.html#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. +4. Specify the Low priority pool using the `process.queue` [directive](https://docs.seqera.io/nextflow/process#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. ### Azure Kubernetes Service (AKS) diff --git a/platform-cloud/docs/troubleshooting_and_faqs/nextflow.md b/platform-cloud/docs/troubleshooting_and_faqs/nextflow.md index adab4bc5d..18ab8bcc6 100644 --- a/platform-cloud/docs/troubleshooting_and_faqs/nextflow.md +++ b/platform-cloud/docs/troubleshooting_and_faqs/nextflow.md @@ -19,7 +19,7 @@ To minimize disruption on existing pipelines, version 22.1.x and later are confi **Invoke Nextflow CLI run arguments during Seqera launch** -From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://www.nextflow.io/docs/latest/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): +From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://docs.seqera.io/nextflow/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): ``` export NXF_CLI_OPTS='-dump-hashes' @@ -43,7 +43,7 @@ Currently, you can resolve this by creating empty `main.nf` and `nextflow.config **Use multiple Nextflow configuration files for different environments** -The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) in the main `nextflow.config`. +The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://docs.seqera.io/nextflow/config#config-profiles) in the main `nextflow.config`. Example: @@ -151,7 +151,7 @@ process.afterScript = 'sleep 60' **Jobs remain in RUNNING status when a pipeline run is canceled** -Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: +Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://docs.seqera.io/nextflow/process#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: ``` process terminateError { @@ -195,7 +195,7 @@ The Groovy shell used by Nextflow to execute your workflow has a hard limit on s 1. Remove any unnecessary code or comments from the script. 2. Move long script bodies into a separate script file in the pipeline `/bin` directory. -3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://www.nextflow.io/docs/latest/dsl2.html#modules). +3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://docs.seqera.io/nextflow/dsl2#modules). ### Nextflow Launcher @@ -224,4 +224,4 @@ If you rely on silent Spot retries (the previous default behavior), you may now - **AWS**: Generic failure with `exit code 1`. You may see messages indicating the host machine was terminated. - **Google**: Spot reclamation typically produces a specific code, but is now surfaced as a recognizable task failure in Nextflow logs. -Since the default for Spot retries is now zero, you must actively enable a retry strategy if you want Nextflow to handle reclaimed Spot instances automatically. For more information, see the [Spot Instance failures and retries](https://www.nextflow.io/docs/latest/updating-spot-retries.html) guide. +Since the default for Spot retries is now zero, you must actively enable a retry strategy if you want Nextflow to handle reclaimed Spot instances automatically. For more information, see the [Spot Instance failures and retries](https://docs.seqera.io/nextflow/updating-spot-retries) guide. diff --git a/platform-cloud/docs/troubleshooting_and_faqs/troubleshooting.md b/platform-cloud/docs/troubleshooting_and_faqs/troubleshooting.md index b60d10424..bc380407e 100644 --- a/platform-cloud/docs/troubleshooting_and_faqs/troubleshooting.md +++ b/platform-cloud/docs/troubleshooting_and_faqs/troubleshooting.md @@ -32,7 +32,7 @@ This error can occur if you execute a DSL1-based Nextflow workflow using [Nextfl The `sleep` commands in your Nextflow workflows may differ in behavior depending on where they are: - If used within an `errorStrategy` block, the Groovy sleep function will be used (which takes its value in milliseconds). -- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://www.nextflow.io/docs/latest/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. +- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://docs.seqera.io/nextflow/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. **Large number of batch job definitions** diff --git a/platform-enterprise_docs/compute-envs/aws-batch.md b/platform-enterprise_docs/compute-envs/aws-batch.md index f0e207873..a0e93594e 100644 --- a/platform-enterprise_docs/compute-envs/aws-batch.md +++ b/platform-enterprise_docs/compute-envs/aws-batch.md @@ -686,7 +686,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM 1. In the **Pipeline work directory** field type or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation), e.g., `s3://seqera-bucket`. The work directory can be customized to specify a folder inside the bucket where Nextflow intermediate files will be stored, e.g., `s3://seqera-bucket/nextflow-workdir`. The bucket must be located in the same region chosen in the previous step. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -695,7 +695,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM Using an EFS or FSx file system as your work directory is currently incompatible with [Studios](../studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
@@ -918,7 +918,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See 1. Select a **Region**, e.g., _eu-west-1 - Europe (Ireland)_. This region must match the region where your S3 bucket or EFS/FSx work directory is located to avoid high data transfer costs. 1. Enter or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation) in the **Pipeline work directory** field, e.g., `s3://seqera-bucket`. This bucket must be in the same region chosen in the previous step to avoid incurring high data transfer costs. The work directory can be customized to specify a folder inside the bucket, e.g., `s3://seqera-bucket/nextflow-workdir`. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -927,7 +927,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See Using an EFS or FSx file system as your work directory is currently incompatible with [Studios](../studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
diff --git a/platform-enterprise_docs/compute-envs/azure-batch.md b/platform-enterprise_docs/compute-envs/azure-batch.md index 2ff6e9605..f2b33121e 100644 --- a/platform-enterprise_docs/compute-envs/azure-batch.md +++ b/platform-enterprise_docs/compute-envs/azure-batch.md @@ -190,7 +190,7 @@ Nextflow can authenticate to Azure services using a managed identity. This metho When you use a manually-configured compute environment with a managed identity attached to the Azure Batch Pool, Nextflow can use this managed identity for authentication. However, Seqera still needs to use access keys or an Entra service principal to submit the initial task to Azure Batch to run Nextflow, which will then proceed with the managed identity for subsequent authentication. 1. In Azure, create a user-assigned managed identity. See [Manage user-assigned managed identities](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-manage-user-assigned-managed-identities) for detailed steps. Take note of the client ID of the managed identity when you create it. -1. The user-assigned managed identity must have the necessary access roles for Nextflow. See [Required role assignments](https://www.nextflow.io/docs/latest/azure.html#required-role-assignments) for more information. +1. The user-assigned managed identity must have the necessary access roles for Nextflow. See [Required role assignments](https://docs.seqera.io/nextflow/azure#required-role-assignments) for more information. 1. Associate the user-assigned managed identity with the Azure Batch Pool. See [Set up managed identity in your Batch pool](https://learn.microsoft.com/en-us/troubleshoot/azure/hpc/batch/use-managed-identities-azure-batch-account-pool#set-up-managed-identity-in-your-batch-pool) for more information. 1. When you set up the Seqera compute environment, select the Azure Batch pool by name and enter the managed identity client ID in the specified field as instructed above. @@ -253,7 +253,7 @@ Create a Batch Forge Azure Batch compute environment: 1. Select a **Region**, such as _eastus_. 1. In the **Pipeline work directory** field, enter the Azure blob container created previously. For example, `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. 1. Select **Enable Fusion v2** to allow access to your Azure Blob Storage data via the [Fusion v2][fusion-docs] virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. @@ -286,7 +286,7 @@ Create a Batch Forge Azure Batch compute environment: 1. Enter the **VMs count**. If autoscaling is enabled (default), this is the maximum number of VMs you wish the pool to scale up to. If autoscaling is disabled, this is the fixed number of virtual machines in the pool. 1. Enable **Autoscale** to scale up and down automatically, based on the number of pipeline tasks. The number of VMs will vary from **0** to **VMs count**. 1. Enable **Dispose resources** for Seqera to automatically delete the Batch pool if the compute environment is deleted on the platform. -1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://www.nextflow.io/docs/latest/wave.html) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. +1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://docs.seqera.io/nextflow/wave) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. 1. Apply [**Resource labels**](../resource-labels/overview). This will populate the **Metadata** fields of the Azure Batch pool. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. @@ -397,7 +397,7 @@ The following settings can be modified after creating a pool: 1. Select a **Region**, such as _eastus (East US)_. 1. In the **Pipeline work directory** field, add the Azure blob container created previously. For example, `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. 1. Select **Enable Fusion v2** to allow access to your Azure Blob Storage data via the [Fusion v2][fusion-docs] virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. @@ -463,7 +463,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [az-vm-gen]: https://learn.microsoft.com/en-us/azure/virtual-machines/generation-2 [az-disk-type]: https://learn.microsoft.com/en-us/azure/virtual-machines/disks-types [az-batch-autoscale]: https://learn.microsoft.com/en-us/azure/batch/batch-automatic-scaling -[az-file-shares]: https://www.nextflow.io/docs/latest/azure.html#azure-file-shares +[az-file-shares]: https://docs.seqera.io/nextflow/azure#azure-file-shares [az-vm-sizes]: https://learn.microsoft.com/en-us/azure/virtual-machines/sizes/overview [wave-docs]: https://docs.seqera.io/wave diff --git a/platform-enterprise_docs/compute-envs/google-cloud-batch.md b/platform-enterprise_docs/compute-envs/google-cloud-batch.md index d277a835e..4fd7c8c49 100644 --- a/platform-enterprise_docs/compute-envs/google-cloud-batch.md +++ b/platform-enterprise_docs/compute-envs/google-cloud-batch.md @@ -147,7 +147,7 @@ Select the **Location** where you will execute your pipelines. See [Location][lo In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the location selected in the previous step. :::note -When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. +When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: #### Seqera features @@ -171,7 +171,7 @@ Select **Enable Fusion v2** to allow access to your Google Cloud Storage data vi :::note To specify virtual machine settings in Platform during compute environment creation, use the **Global Nextflow config** field to apply custom Nextflow process directives to all pipeline runs launched with this compute environment. - To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://www.nextflow.io/docs/latest/google.html#process-definition) for more information. + To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://docs.seqera.io/nextflow/google#process-definition) for more information. ::: When Fusion v2 is enabled, the following virtual machine settings are applied: @@ -231,7 +231,7 @@ If you use VM instance templates for the head or compute jobs (see step 6 below) :::caution Seqera does not validate the VM instance template you specify in these fields. Generally, use templates that define only the machine type, network, disk, and configuration values that will not change across multiple VM instances and Seqera compute environments. See [Create instance templates](https://cloud.google.com/compute/docs/instance-templates/create-instance-templates) for instructions to create your instance templates. - To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://www.nextflow.io/docs/latest/google.html#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://www.nextflow.io/docs/latest/config.html#config-process-selectors) to assign separate templates to each of your processes. + To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://docs.seqera.io/nextflow/google#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://docs.seqera.io/nextflow/config#config-process-selectors) to assign separate templates to each of your processes. ::: Select **Create** to finalize the compute environment setup. @@ -244,7 +244,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [create-sa]: https://cloud.google.com/iam/docs/service-accounts-create#creating [get-json]: https://cloud.google.com/iam/docs/keys-list-get#get-key [location]: https://cloud.google.com/compute/docs/regions-zones#available -[wave-docs]: https://www.nextflow.io/docs/latest/wave.html +[wave-docs]: https://docs.seqera.io/nextflow/wave [fusion-docs]: https://docs.seqera.io/fusion [platform-fusion-docs]: ../supported_software/fusion/overview [pre-post-run-scripts]: ../launch/advanced#pre-and-post-run-scripts diff --git a/platform-enterprise_docs/compute-envs/hpc.md b/platform-enterprise_docs/compute-envs/hpc.md index 3c18037a1..98cd817b8 100644 --- a/platform-enterprise_docs/compute-envs/hpc.md +++ b/platform-enterprise_docs/compute-envs/hpc.md @@ -64,8 +64,8 @@ To create a new **HPC** compute environment: 1. Enter the absolute path of the **Launch directory** to be used on the cluster. If omitted, it will be the same as the work directory. 1. Enter the **Login hostname**. This is usually the hostname or public IP address of the cluster's login node. -1. Enter the **Head queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will be submitted. -1. Enter the **Compute queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will submit tasks. +1. Enter the **Head queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will be submitted. +1. Enter the **Compute queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will submit tasks. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. diff --git a/platform-enterprise_docs/compute-envs/overview.md b/platform-enterprise_docs/compute-envs/overview.md index b888a301c..4d3a1d6cb 100644 --- a/platform-enterprise_docs/compute-envs/overview.md +++ b/platform-enterprise_docs/compute-envs/overview.md @@ -49,8 +49,8 @@ Some important considerations: - Seqera only supports NVIDIA GPUs. Select instances with NVIDIA GPUs for your GPU-dependent processes. - The **Enable GPUs** setting causes Batch Forge to specify the most current [AWS-recommended GPU-optimized ECS AMI](https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ecs-optimized_AMI.html) as the EC2 fleet AMI when creating the compute environment. This setting can be overridden by **AMI ID** in the advanced options. - The **Enable GPUs** setting alone does not deploy GPU instances in your compute environment. You must still specify GPU-enabled instance types in the **Advanced options > Instance types** field. -- Your Nextflow script must include [accelerator directives](https://www.nextflow.io/docs/latest/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. -- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: +- Your Nextflow script must include [accelerator directives](https://docs.seqera.io/nextflow/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. +- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://docs.seqera.io/nextflow/process#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: ```groovy process { diff --git a/platform-enterprise_docs/credentials/aws_registry_credentials.md b/platform-enterprise_docs/credentials/aws_registry_credentials.md index 337f109ec..15f17af93 100644 --- a/platform-enterprise_docs/credentials/aws_registry_credentials.md +++ b/platform-enterprise_docs/credentials/aws_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [aws, ecr, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_docs/credentials/azure_registry_credentials.md b/platform-enterprise_docs/credentials/azure_registry_credentials.md index 47e0184b7..a35a15b43 100644 --- a/platform-enterprise_docs/credentials/azure_registry_credentials.md +++ b/platform-enterprise_docs/credentials/azure_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [azure, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_docs/credentials/docker_hub_registry_credentials.md b/platform-enterprise_docs/credentials/docker_hub_registry_credentials.md index 1c1e376d6..8ce8339a4 100644 --- a/platform-enterprise_docs/credentials/docker_hub_registry_credentials.md +++ b/platform-enterprise_docs/credentials/docker_hub_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [docker, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_docs/credentials/gitea_registry_credentials.md b/platform-enterprise_docs/credentials/gitea_registry_credentials.md index 68942d36e..83f4668ed 100644 --- a/platform-enterprise_docs/credentials/gitea_registry_credentials.md +++ b/platform-enterprise_docs/credentials/gitea_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [gitea, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). Gitea container registries support [authentication][gitea-auth] using a personal access token. Use your personal access token as your password when you create your Gitea container registry credentials in Seqera. diff --git a/platform-enterprise_docs/credentials/github_registry_credentials.md b/platform-enterprise_docs/credentials/github_registry_credentials.md index e69de52aa..f24937d55 100644 --- a/platform-enterprise_docs/credentials/github_registry_credentials.md +++ b/platform-enterprise_docs/credentials/github_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [github, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). GitHub Packages only supports [authentication][github-pat] using a personal access token (classic). Use your personal access token as your password when you create your GitHub container registry credentials in Seqera. diff --git a/platform-enterprise_docs/credentials/gitlab_registry_credentials.md b/platform-enterprise_docs/credentials/gitlab_registry_credentials.md index 39a91e0bc..ff4e1ace0 100644 --- a/platform-enterprise_docs/credentials/gitlab_registry_credentials.md +++ b/platform-enterprise_docs/credentials/gitlab_registry_credentials.md @@ -5,7 +5,7 @@ date: "2023-12-15" tags: [gitlab, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). If your organization enabled two-factor authentication (2FA) for your GitLab organization or project, you must use your [personal access token][gitlab-pat] as your password when you create your [GitLab container registry credentials][gitlab-cr]. diff --git a/platform-enterprise_docs/credentials/google_registry_credentials.md b/platform-enterprise_docs/credentials/google_registry_credentials.md index f6487e1e1..f580d30e1 100644 --- a/platform-enterprise_docs/credentials/google_registry_credentials.md +++ b/platform-enterprise_docs/credentials/google_registry_credentials.md @@ -5,7 +5,7 @@ date: "2023-04-21" tags: [google, container, registry, artifact, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_docs/credentials/quay_registry_credentials.md b/platform-enterprise_docs/credentials/quay_registry_credentials.md index 9a160b73d..93563fa32 100644 --- a/platform-enterprise_docs/credentials/quay_registry_credentials.md +++ b/platform-enterprise_docs/credentials/quay_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [quay, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_docs/enterprise/advanced-topics/manual-azure-batch-setup.md b/platform-enterprise_docs/enterprise/advanced-topics/manual-azure-batch-setup.md index 4e7c9894d..473311c80 100644 --- a/platform-enterprise_docs/enterprise/advanced-topics/manual-azure-batch-setup.md +++ b/platform-enterprise_docs/enterprise/advanced-topics/manual-azure-batch-setup.md @@ -320,7 +320,7 @@ Select **Launch** next to the `hello-world-autopool-low-priority` pipeline in yo Seqera can utilize an Azure Entra service principal to authenticate and access Azure Batch for job execution and Azure Storage for data management, and Nextflow can authenticate to Azure services using a managed identity. This method offers enhanced security compared to access keys, but must run on Azure infrastructure. -See [Microsoft Entra](https://www.nextflow.io/docs/latest/azure.html#microsoft-entra) in the Nextflow documentation for more information. +See [Microsoft Entra](https://docs.seqera.io/nextflow/azure#microsoft-entra) in the Nextflow documentation for more information. #### Create a service principal for Seqera to use for authentication @@ -340,7 +340,7 @@ In Seqera: Back in the Azure Portal: 1. [Create a managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-manage-user-assigned-managed-identities?pivots=identity-mi-methods-azp) -1. [Assign the relevant roles to the managed identity](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current). See [Required role assignments](https://www.nextflow.io/docs/latest/azure.html#required-role-assignments) for Nextflow requirements. +1. [Assign the relevant roles to the managed identity](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current). See [Required role assignments](https://docs.seqera.io/nextflow/azure#required-role-assignments) for Nextflow requirements. 1. Note the managed identity client ID for later. 1. In the Azure Portal, go to the Batch account you created earlier. 1. Go to the **Pools** tab and find the pool called `tower-pool-${id}`, where `${id}` is the ID of the head node pool created earlier. @@ -481,6 +481,6 @@ If you wish to keep the Azure resources, you can remove each pool within a Batch [install-azure-cli]: https://learn.microsoft.com/en-us/cli/azure/install-azure-cli [install-seqera-cli]: /platform-cli/installation -[nextflow-working-directory]: https://www.nextflow.io/docs/latest/cache-and-resume.html#work-directory +[nextflow-working-directory]: https://docs.seqera.io/nextflow/cache-and-resume#work-directory [create-org-workspace]: ../../getting-started/workspace-setup [add-pipeline]: ../../getting-started/quickstart-demo/add-pipelines#add-from-the-launchpad diff --git a/platform-enterprise_docs/enterprise/configuration/wave.md b/platform-enterprise_docs/enterprise/configuration/wave.md index b84fe0534..8d84565f1 100644 --- a/platform-enterprise_docs/enterprise/configuration/wave.md +++ b/platform-enterprise_docs/enterprise/configuration/wave.md @@ -79,5 +79,5 @@ See the [Wave documentation](https://docs.seqera.io/wave) for installation and c ## Additional resources - [Wave documentation](https://docs.seqera.io/wave) -- [Nextflow Wave integration](https://www.nextflow.io/docs/latest/wave.html) +- [Nextflow Wave integration](https://docs.seqera.io/nextflow/wave) - [Seqera Containers](https://seqera.io/containers/) - Free community container registry diff --git a/platform-enterprise_docs/getting-started/deployment-options.md b/platform-enterprise_docs/getting-started/deployment-options.md index 7fe24fd1a..49e4f2f87 100644 --- a/platform-enterprise_docs/getting-started/deployment-options.md +++ b/platform-enterprise_docs/getting-started/deployment-options.md @@ -86,5 +86,5 @@ If you have an existing environment where you run Nextflow directly, you can sti You can now monitor your workflow runs in the Seqera interface. To configure and execute Nextflow pipelines in cloud environments, see [compute environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-enterprise_docs/getting-started/proteinfold.md b/platform-enterprise_docs/getting-started/proteinfold.md index c3f52ced6..385bcbb14 100644 --- a/platform-enterprise_docs/getting-started/proteinfold.md +++ b/platform-enterprise_docs/getting-started/proteinfold.md @@ -185,7 +185,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL: `https://github.com/nf-core/proteinfold`. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name: `1.1.1`. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-enterprise_docs/getting-started/quickstart-demo/launch-pipelines.md b/platform-enterprise_docs/getting-started/quickstart-demo/launch-pipelines.md index ddbc10c08..5615cc7a3 100644 --- a/platform-enterprise_docs/getting-started/quickstart-demo/launch-pipelines.md +++ b/platform-enterprise_docs/getting-started/quickstart-demo/launch-pipelines.md @@ -49,7 +49,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc :::info See [Git revision management](../../pipelines/revision.md) for more information on **Commit ID**, **Pull latest**, and **Revision** behavior. ::: -- (*Optional*) **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. +- (*Optional*) **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - (*Optional*) **Labels**: Assign new or existing [labels](../../labels/overview) to the run. - **Compute environment**: Select an existing workspace [compute environment](../../compute-envs/overview). diff --git a/platform-enterprise_docs/getting-started/rnaseq.md b/platform-enterprise_docs/getting-started/rnaseq.md index b08c961b0..60ef78419 100644 --- a/platform-enterprise_docs/getting-started/rnaseq.md +++ b/platform-enterprise_docs/getting-started/rnaseq.md @@ -196,7 +196,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-enterprise_docs/launch/advanced.md b/platform-enterprise_docs/launch/advanced.md index 714f50a43..7a6060212 100644 --- a/platform-enterprise_docs/launch/advanced.md +++ b/platform-enterprise_docs/launch/advanced.md @@ -10,7 +10,7 @@ You can modify the configuration and execution of a pipeline with advanced launc ### Nextflow config file -Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://www.nextflow.io/docs/latest/config.html#config-syntax). +Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax). For example, modify the **manifest** section to give the pipeline a name and description that will show up in the Seqera monitoring section: @@ -127,7 +127,7 @@ Instruct Nextflow to pull the latest pipeline version from the Git repository. T ### Stub run -Replace Nextflow process commands with command [stubs](https://www.nextflow.io/docs/latest/process.html#stub), where defined, before execution. +Replace Nextflow process commands with command [stubs](https://docs.seqera.io/nextflow/process#stub), where defined, before execution. ### Main script diff --git a/platform-enterprise_docs/launch/cache-resume.mdx b/platform-enterprise_docs/launch/cache-resume.mdx index 558b0d2ad..ef47bd4d2 100644 --- a/platform-enterprise_docs/launch/cache-resume.mdx +++ b/platform-enterprise_docs/launch/cache-resume.mdx @@ -8,13 +8,13 @@ tags: [cache, launch, resume, relaunch] import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; -Nextflow maintains a [cache](https://www.nextflow.io/docs/latest/cache-and-resume.html) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. +Nextflow maintains a [cache](https://docs.seqera.io/nextflow/cache-and-resume) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. ## Cache directory -Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. +Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. -To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://www.nextflow.io/docs/latest/process.html#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). +To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://docs.seqera.io/nextflow/process#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). @@ -108,7 +108,7 @@ Kubernetes compute environments do not use cloud cache by default. To specify a Google Cloud Storage 1. See [these instructions](../compute-envs/google-cloud-batch#iam) to set up IAM and create a JSON key file for the custom service account with permissions to your Google Cloud storage account. - 2. If you run the [gcloud CLI authentication flow](https://nextflow.io/docs/edge/google.html#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. + 2. If you run the [gcloud CLI authentication flow](https://docs.seqera.io/nextflow/google#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. 3. Add the following to the **Nextflow Config file** field when you [launch](../launch/launchpad#launch-form) your pipeline: ```groovy diff --git a/platform-enterprise_docs/launch/launchpad.md b/platform-enterprise_docs/launch/launchpad.md index 7189fe720..0c2310afa 100644 --- a/platform-enterprise_docs/launch/launchpad.md +++ b/platform-enterprise_docs/launch/launchpad.md @@ -33,7 +33,7 @@ The launch form accepts URL query parameters. See [Populate launch form with URL - **Pipeline to launch**: A Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. Private repositories require [access credentials](../credentials/overview). :::note - Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://www.nextflow.io/docs/latest/sharing.html) in the Nextflow docs for more details. + Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://docs.seqera.io/nextflow/sharing) in the Nextflow docs for more details. ::: - **Revision**: A valid repository commit ID, tag, or branch name. Determines the version of the pipeline to launch. - **Commit ID**: Pin pipeline revision to the most recent HEAD commit ID. If no commit ID is pinned, the latest revision of the repository branch or tag is used. @@ -41,7 +41,7 @@ The launch form accepts URL query parameters. See [Populate launch form with URL :::info See [Git revision management](../pipelines/revision.md) for more information on **Commit ID**, **Pull latest**, and **Revision** behavior. ::: -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: A unique identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: The [compute environment](../compute-envs/overview) where the run will be launched. @@ -116,7 +116,7 @@ Use resource labels to tag the computing resources created during the workflow e Secrets are used to store keys and tokens used by workflow tasks to interact with external systems. Enter the names of any stored user or workspace secrets required for the workflow execution. :::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: #### Advanced options diff --git a/platform-enterprise_docs/monitoring/overview.md b/platform-enterprise_docs/monitoring/overview.md index 53b40928e..6a9e1b66e 100644 --- a/platform-enterprise_docs/monitoring/overview.md +++ b/platform-enterprise_docs/monitoring/overview.md @@ -13,7 +13,7 @@ The **Runs** tab contains all previous runs in the workspace. Each new or resume - `submitted`: Pending execution - `running`: Running - `succeeded`: Completed successfully -- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://www.nextflow.io/docs/latest/process.html#errorstrategy) +- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://docs.seqera.io/nextflow/process#errorstrategy) - `cancelled`: Stopped manually during execution - `unknown`: Indeterminate status diff --git a/platform-enterprise_docs/pipelines/overview.md b/platform-enterprise_docs/pipelines/overview.md index afc7283a0..dac5e2e68 100644 --- a/platform-enterprise_docs/pipelines/overview.md +++ b/platform-enterprise_docs/pipelines/overview.md @@ -11,7 +11,7 @@ When you add a pipeline to Seqera, you define: - The pipeline Git repository and [revision](./revision.md) (branch, tag, or commit) - [Compute environment](../compute-envs/overview.md) for execution -- Pipeline parameters and [configuration profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) +- Pipeline parameters and [configuration profiles](https://docs.seqera.io/nextflow/config#config-profiles) - (Optional) [Labels](../labels/overview.md), [resource labels](../resource-labels/overview.md), and [secrets](../secrets/overview.md) - (Optional) [Pre-run and post-run](../launch/advanced.md#pre-and-post-run-scripts) bash scripts that execute in your compute environment diff --git a/platform-enterprise_docs/platform-enterprise.md b/platform-enterprise_docs/platform-enterprise.md index e32595db8..bc837db8f 100644 --- a/platform-enterprise_docs/platform-enterprise.md +++ b/platform-enterprise_docs/platform-enterprise.md @@ -29,4 +29,4 @@ Request a [**demo**](https://seqera.io/demo "Seqera Enterprise Demo") to explore Nextflow is both a programming workflow language and an execution runtime that supports a wide range of execution platforms, including popular traditional grid scheduling systems such as Slurm and IBM LSF, and cloud services such as AWS, Azure, and Google Cloud Batch. -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/) to learn more. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/) to learn more. diff --git a/platform-enterprise_docs/reports/overview.md b/platform-enterprise_docs/reports/overview.md index c4ba99b1c..59db26855 100644 --- a/platform-enterprise_docs/reports/overview.md +++ b/platform-enterprise_docs/reports/overview.md @@ -82,10 +82,10 @@ By default, the MIME type is deduced from the file extension, so you don't need Nextflow can generate a number of built-in reports: -- [Execution report](https://nextflow.io/docs/latest/tracing.html#execution-report) -- [Execution timeline](https://nextflow.io/docs/latest/tracing.html#timeline-report) -- [Trace file](https://nextflow.io/docs/latest/tracing.html#trace-report) -- [Workflow diagram](https://nextflow.io/docs/latest/tracing.html#dag-visualisation) (i.e. DAG) +- [Execution report](https://docs.seqera.io/nextflow/tracing#execution-report) +- [Execution timeline](https://docs.seqera.io/nextflow/tracing#timeline-report) +- [Trace file](https://docs.seqera.io/nextflow/tracing#trace-report) +- [Workflow diagram](https://docs.seqera.io/nextflow/tracing#dag-visualisation) (i.e. DAG) In Nextflow version 24.03.0-edge and later, these reports can be included as pipeline reports in Seqera Platform. Specify them in `tower.yml` like any other file: diff --git a/platform-enterprise_docs/secrets/overview.md b/platform-enterprise_docs/secrets/overview.md index e6498a5fd..c5c1d130a 100644 --- a/platform-enterprise_docs/secrets/overview.md +++ b/platform-enterprise_docs/secrets/overview.md @@ -31,12 +31,12 @@ Secrets defined by a user have higher priority and will override any secrets wit ## Use secrets in workflows -When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://www.nextflow.io/docs/edge/secrets.html#process-secrets) for more information. +When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://docs.seqera.io/nextflow/secrets) for more information. Secrets are automatically deleted from the secret manager when the pipeline completes, successfully or unsuccessfully. :::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: ## AWS Secrets Manager integration diff --git a/platform-enterprise_docs/supported_software/dragen/overview.md b/platform-enterprise_docs/supported_software/dragen/overview.md index 90b17c409..0ab3e9023 100644 --- a/platform-enterprise_docs/supported_software/dragen/overview.md +++ b/platform-enterprise_docs/supported_software/dragen/overview.md @@ -80,7 +80,7 @@ See the [dragen.nf](https://github.com/seqeralabs/nf-dragen/blob/master/modules/ } ``` - See the [Nextflow label docs](https://www.nextflow.io/docs/latest/process.html?highlight=label#label) for more information. + See the [Nextflow label docs](https://docs.seqera.io/nextflow/process.html?highlight=label#label) for more information. 2. Define secrets in Seqera: diff --git a/platform-enterprise_docs/troubleshooting_and_faqs/azure_troubleshooting.md b/platform-enterprise_docs/troubleshooting_and_faqs/azure_troubleshooting.md index bf88be612..62b10f218 100644 --- a/platform-enterprise_docs/troubleshooting_and_faqs/azure_troubleshooting.md +++ b/platform-enterprise_docs/troubleshooting_and_faqs/azure_troubleshooting.md @@ -16,12 +16,12 @@ The default Azure Batch implementation in Seqera Platform uses a single pool for - One [Low priority](https://learn.microsoft.com/en-us/azure/batch/batch-spot-vms#differences-between-spot-and-low-priority-vms) :::note -Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://www.nextflow.io/docs/latest/azure.html#requirements-on-pre-existing-named-pools). +Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://docs.seqera.io/nextflow/azure#requirements-on-pre-existing-named-pools). ::: 2. Create a manual [Azure Batch](../compute-envs/azure-batch#manual) compute environment in Seqera Platform. 3. In **Compute pool name**, specify your dedicated Batch pool. -4. Specify the Low priority pool using the `process.queue` [directive](https://www.nextflow.io/docs/latest/process.html#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. +4. Specify the Low priority pool using the `process.queue` [directive](https://docs.seqera.io/nextflow/process#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. ### Azure Kubernetes Service (AKS) diff --git a/platform-enterprise_docs/troubleshooting_and_faqs/nextflow.md b/platform-enterprise_docs/troubleshooting_and_faqs/nextflow.md index e8003814e..89d0feeba 100644 --- a/platform-enterprise_docs/troubleshooting_and_faqs/nextflow.md +++ b/platform-enterprise_docs/troubleshooting_and_faqs/nextflow.md @@ -20,7 +20,7 @@ To minimize disruption on existing pipelines, version 22.1.x and later are confi **Invoke Nextflow CLI run arguments during Seqera launch** -From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://www.nextflow.io/docs/latest/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): +From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://docs.seqera.io/nextflow/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): ``` export NXF_CLI_OPTS='-dump-hashes' @@ -44,7 +44,7 @@ Currently, you can resolve this by creating empty `main.nf` and `nextflow.config **Use multiple Nextflow configuration files for different environments** -The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) in the main `nextflow.config`. +The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://docs.seqera.io/nextflow/config#config-profiles) in the main `nextflow.config`. Example: @@ -152,7 +152,7 @@ process.afterScript = 'sleep 60' **Jobs remain in RUNNING status when a pipeline run is canceled** -Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: +Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://docs.seqera.io/nextflow/process#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: ``` process terminateError { @@ -196,7 +196,7 @@ The Groovy shell used by Nextflow to execute your workflow has a hard limit on s 1. Remove any unnecessary code or comments from the script. 2. Move long script bodies into a separate script file in the pipeline `/bin` directory. -3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://www.nextflow.io/docs/latest/dsl2.html#modules). +3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://docs.seqera.io/nextflow/dsl2#modules). ### Nextflow Launcher diff --git a/platform-enterprise_docs/troubleshooting_and_faqs/troubleshooting.md b/platform-enterprise_docs/troubleshooting_and_faqs/troubleshooting.md index 019f2dc62..b044e6068 100644 --- a/platform-enterprise_docs/troubleshooting_and_faqs/troubleshooting.md +++ b/platform-enterprise_docs/troubleshooting_and_faqs/troubleshooting.md @@ -47,7 +47,7 @@ This error can occur if you execute a DSL1-based Nextflow workflow using [Nextfl The `sleep` commands in your Nextflow workflows may differ in behavior depending on where they are: - If used within an `errorStrategy` block, the Groovy sleep function will be used (which takes its value in milliseconds). -- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://www.nextflow.io/docs/latest/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. +- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://docs.seqera.io/nextflow/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. **Large number of batch job definitions** diff --git a/platform-enterprise_versioned_docs/version-22.4/compute-envs/altair-grid-engine.md b/platform-enterprise_versioned_docs/version-22.4/compute-envs/altair-grid-engine.md index 40a3bb60b..e99852b9b 100644 --- a/platform-enterprise_versioned_docs/version-22.4/compute-envs/altair-grid-engine.md +++ b/platform-enterprise_versioned_docs/version-22.4/compute-envs/altair-grid-engine.md @@ -15,7 +15,7 @@ To launch pipelines into a **Grid Engine** cluster from Tower, the following req - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ### Compute Environment @@ -42,7 +42,7 @@ To create a new compute environment for **Grid Engine** in Tower: 10. Enter the **Compute queue name**, the cluster queue to which the Nextflow job will submit tasks. :::tip - The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [docs](https://www.nextflow.io/docs/latest/process.html#queue) for more details. + The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [docs](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. You can use the **Environment variables** option to specify custom environment variables for the Head job and/or Compute jobs. diff --git a/platform-enterprise_versioned_docs/version-22.4/compute-envs/altair-pbs-pro.md b/platform-enterprise_versioned_docs/version-22.4/compute-envs/altair-pbs-pro.md index bf50f6879..9ebdc8610 100644 --- a/platform-enterprise_versioned_docs/version-22.4/compute-envs/altair-pbs-pro.md +++ b/platform-enterprise_versioned_docs/version-22.4/compute-envs/altair-pbs-pro.md @@ -15,7 +15,7 @@ To launch pipelines into a **PBS Pro** cluster from Tower, the following require - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ### Compute Environment @@ -42,7 +42,7 @@ To create a new compute environment for **PBS Pro** in Tower: 10. Enter the **Compute queue name**, the cluster queue to which the Nextflow job will submit tasks. :::tip - The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [docs](https://www.nextflow.io/docs/latest/process.html#queue) for more details. + The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [docs](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. You can use the **Environment variables** option to specify custom environment variables for the Head job and/or Compute jobs. diff --git a/platform-enterprise_versioned_docs/version-22.4/compute-envs/lsf.md b/platform-enterprise_versioned_docs/version-22.4/compute-envs/lsf.md index 653d8196f..86d925cf5 100644 --- a/platform-enterprise_versioned_docs/version-22.4/compute-envs/lsf.md +++ b/platform-enterprise_versioned_docs/version-22.4/compute-envs/lsf.md @@ -15,7 +15,7 @@ To launch pipelines into an **LSF** cluster from Tower, the following requiremen - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ### Compute Environment @@ -42,7 +42,7 @@ To create a new compute environment for **LSF** in Tower: 10. Enter the **Compute queue name**, the cluster queue to which the Nextflow job will submit tasks. :::tip - The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [docs](https://www.nextflow.io/docs/latest/process.html#queue) for more details. + The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [docs](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. You can use the **Environment variables** option to specify custom environment variables for the Head job and/or Compute jobs. diff --git a/platform-enterprise_versioned_docs/version-22.4/compute-envs/moab.md b/platform-enterprise_versioned_docs/version-22.4/compute-envs/moab.md index fb0b6a781..606d818ba 100644 --- a/platform-enterprise_versioned_docs/version-22.4/compute-envs/moab.md +++ b/platform-enterprise_versioned_docs/version-22.4/compute-envs/moab.md @@ -15,7 +15,7 @@ To launch pipelines into a **Moab** cluster from Tower, the following requiremen - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ### Compute Environment @@ -42,7 +42,7 @@ To create a new compute environment for **Moab** in Tower: 10. Enter the **Compute queue name**, the cluster queue to which the Nextflow job will submit tasks. :::tip - The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [docs](https://www.nextflow.io/docs/latest/process.html#queue) for more details. + The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [docs](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. You can use the **Environment variables** option to specify custom environment variables for the Head job and/or Compute jobs. diff --git a/platform-enterprise_versioned_docs/version-22.4/compute-envs/overview.md b/platform-enterprise_versioned_docs/version-22.4/compute-envs/overview.md index 8dd47a1c4..90b8f3442 100644 --- a/platform-enterprise_versioned_docs/version-22.4/compute-envs/overview.md +++ b/platform-enterprise_versioned_docs/version-22.4/compute-envs/overview.md @@ -46,7 +46,7 @@ The AWS Batch compute environment creation form in Tower includes an **Enable GP - This setting can be overridden by **AMI ID** in the advanced options. -- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: +- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://docs.seqera.io/nextflow/process#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: ```groovy process { diff --git a/platform-enterprise_versioned_docs/version-22.4/compute-envs/slurm.md b/platform-enterprise_versioned_docs/version-22.4/compute-envs/slurm.md index 419d12224..05a7c6a2b 100644 --- a/platform-enterprise_versioned_docs/version-22.4/compute-envs/slurm.md +++ b/platform-enterprise_versioned_docs/version-22.4/compute-envs/slurm.md @@ -15,7 +15,7 @@ To launch pipelines into a **Slurm** cluster from Tower, the following requireme - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ### Compute Environment @@ -42,7 +42,7 @@ To create a new compute environment for **Slurm** in Tower: 10. Enter the **Compute queue name**, the cluster queue to which the Nextflow job will submit tasks. :::tip - The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [docs](https://www.nextflow.io/docs/latest/process.html#queue) for more details. + The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [docs](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. You can use the **Environment variables** option to specify custom environment variables for the Head job and/or Compute jobs. diff --git a/platform-enterprise_versioned_docs/version-22.4/credentials/aws_registry_credentials.md b/platform-enterprise_versioned_docs/version-22.4/credentials/aws_registry_credentials.md index d12ee72b3..ce489e0c5 100644 --- a/platform-enterprise_versioned_docs/version-22.4/credentials/aws_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-22.4/credentials/aws_registry_credentials.md @@ -6,7 +6,7 @@ description: "Step-by-step instructions to set up AWS ECR credentials in Nextflo ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-22.4/credentials/azure_registry_credentials.md b/platform-enterprise_versioned_docs/version-22.4/credentials/azure_registry_credentials.md index 24eb6702b..c2309e72d 100644 --- a/platform-enterprise_versioned_docs/version-22.4/credentials/azure_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-22.4/credentials/azure_registry_credentials.md @@ -6,7 +6,7 @@ description: "Step-by-step instructions to set up Azure container registry crede ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-22.4/credentials/docker_hub_registry_credentials.md b/platform-enterprise_versioned_docs/version-22.4/credentials/docker_hub_registry_credentials.md index 848f22e70..43b6c3a28 100644 --- a/platform-enterprise_versioned_docs/version-22.4/credentials/docker_hub_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-22.4/credentials/docker_hub_registry_credentials.md @@ -6,7 +6,7 @@ description: "Step-by-step instructions to set up Docker container registry cred ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-22.4/credentials/google_registry_credentials.md b/platform-enterprise_versioned_docs/version-22.4/credentials/google_registry_credentials.md index 3a4b47e10..b94add10e 100644 --- a/platform-enterprise_versioned_docs/version-22.4/credentials/google_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-22.4/credentials/google_registry_credentials.md @@ -6,7 +6,7 @@ description: "Step-by-step instructions to set up Google Cloud registry credenti ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-22.4/credentials/quay_registry_credentials.md b/platform-enterprise_versioned_docs/version-22.4/credentials/quay_registry_credentials.md index df2d85d57..7e5be129d 100644 --- a/platform-enterprise_versioned_docs/version-22.4/credentials/quay_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-22.4/credentials/quay_registry_credentials.md @@ -6,7 +6,7 @@ description: "Step-by-step instructions to set up Quay container credentials in ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-22.4/faqs.md b/platform-enterprise_versioned_docs/version-22.4/faqs.md index da2e63af1..dddd03ce8 100644 --- a/platform-enterprise_versioned_docs/version-22.4/faqs.md +++ b/platform-enterprise_versioned_docs/version-22.4/faqs.md @@ -125,7 +125,7 @@ This error can occur if you execute a DSL 1-based Nextflow workflow using [Nextf The `sleep` commands within your Nextflow workflows may differ in behaviour depending on where they are: - If used within an `errorStrategy` block, the Groovy sleep function will be used (which takes its value in milliseconds). -- If used within a process script block, that language's sleep binary/method will be used. **Example:** [this BASH script](https://www.nextflow.io/docs/latest/metrics.html?highlight=sleep) uses the BASH sleep binary, which takes its value in seconds. +- If used within a process script block, that language's sleep binary/method will be used. **Example:** [this BASH script](https://docs.seqera.io/nextflow/metrics.html?highlight=sleep) uses the BASH sleep binary, which takes its value in seconds. **

Q: Why does re-launching/resuming a run fail with `field revision is not writable`?

** @@ -402,7 +402,7 @@ To resolve the issue, please try reloading the UI to reinitiate the client's con **

Q: How can I specify Nextflow CLI run arguments when launching from Tower?

** -As of Nextflow v22.09.1-edge, when invoking a pipeline from Tower, you can specify [Nextflow CLI run arguments](https://www.nextflow.io/docs/latest/cli.html?highlight=dump#run) by setting the `NXF_CLI_OPTS` environment variable via pre-run script: +As of Nextflow v22.09.1-edge, when invoking a pipeline from Tower, you can specify [Nextflow CLI run arguments](https://docs.seqera.io/nextflow/cli.html?highlight=dump#run) by setting the `NXF_CLI_OPTS` environment variable via pre-run script: ``` # Example: @@ -431,7 +431,7 @@ Current as of May 16, 2022, there is no solution for this problem other than to **

Q: Is it possible to maintain different Nextflow configuration files for different environments?

** -Yes. The main `nextflow.config` file will always be imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [their own profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) in the main `nextflow.config`. +Yes. The main `nextflow.config` file will always be imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [their own profile](https://docs.seqera.io/nextflow/config#config-profiles) in the main `nextflow.config`. Example: @@ -543,7 +543,7 @@ process.afterScript = 'sleep 60' **

Q: Why are jobs in RUNNING status not terminated when my pipeline run is canceled?

** -The behavior of Tower when canceling a run depends on the [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: +The behavior of Tower when canceling a run depends on the [`errorStrategy`](https://docs.seqera.io/nextflow/process#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: ```bash @@ -792,7 +792,7 @@ Note: 1. Activation does not cause GPU-enabled instances to automatically spawn in your Batch cluster. You must still specify these in the Forge screen's **Advanced options > Instance types** field. 2. Population of the Forge screen's **Advanced options > AMI Id** field will supersede the AWS-recommended AMI. -3. Your Nextflow script must include [accelerator directives](https://www.nextflow.io/docs/latest/process.html?highlight=accelerator) to use the provisioned GPUs. +3. Your Nextflow script must include [accelerator directives](https://docs.seqera.io/nextflow/process.html?highlight=accelerator) to use the provisioned GPUs. ### tw CLI diff --git a/platform-enterprise_versioned_docs/version-22.4/getting-started/usage.md b/platform-enterprise_versioned_docs/version-22.4/getting-started/usage.md index b299f4455..dd53e92af 100644 --- a/platform-enterprise_versioned_docs/version-22.4/getting-started/usage.md +++ b/platform-enterprise_versioned_docs/version-22.4/getting-started/usage.md @@ -73,5 +73,5 @@ The token will only be displayed once. You must copy and save the token before c To configure and execute Nextflow pipelines in cloud environments, see [Compute Environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-enterprise_versioned_docs/version-22.4/launch/advanced.md b/platform-enterprise_versioned_docs/version-22.4/launch/advanced.md index ea900b471..9a57ec1e3 100644 --- a/platform-enterprise_versioned_docs/version-22.4/launch/advanced.md +++ b/platform-enterprise_versioned_docs/version-22.4/launch/advanced.md @@ -10,7 +10,7 @@ Advanced launch options allow users to modify the configuration and execution of The _Nextflow config_ field allows the addition of settings to the Nextflow configuration file. -This text should follow the same syntax as the [Nextflow configuration file](https://www.nextflow.io/docs/latest/config.html#config-syntax). +This text should follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax). In the example below, we can modify the **manifest** section to give the pipeline a name and description which will show up in the Tower monitoring section. diff --git a/platform-enterprise_versioned_docs/version-22.4/launch/launch-form.md b/platform-enterprise_versioned_docs/version-22.4/launch/launch-form.md index 3394937ea..b86081297 100644 --- a/platform-enterprise_versioned_docs/version-22.4/launch/launch-form.md +++ b/platform-enterprise_versioned_docs/version-22.4/launch/launch-form.md @@ -19,7 +19,7 @@ To launch a pipeline: 3. Enter a repository URL for the **Pipeline to launch** (e.g. `https://github.com/nf-core/rnaseq.git`). :::tip -Nextflow pipelines are just Git repositories and they can reside on any public or private Git-hosting platform. See [Git Integration](../git/overview) in the Tower docs and [Pipeline Sharing](https://www.nextflow.io/docs/latest/sharing.html) in the Nextflow docs for more details. +Nextflow pipelines are just Git repositories and they can reside on any public or private Git-hosting platform. See [Git Integration](../git/overview) in the Tower docs and [Pipeline Sharing](https://docs.seqera.io/nextflow/sharing) in the Nextflow docs for more details. ::: 4. You can select a **Revision number** to use a specific version of the pipeline. @@ -36,7 +36,7 @@ The credentials associated with the compute environment must be able to access t 6. Select any **Config profiles** you would like to use. - Visit the Nextflow [Config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) documentation for more details. + Visit the Nextflow [Config profiles](https://docs.seqera.io/nextflow/config#config-profiles) documentation for more details. 7. Enter any **Pipeline parameters** in YAML or JSON format. diff --git a/platform-enterprise_versioned_docs/version-22.4/secrets/overview.md b/platform-enterprise_versioned_docs/version-22.4/secrets/overview.md index cd0fadfee..9a59148eb 100644 --- a/platform-enterprise_versioned_docs/version-22.4/secrets/overview.md +++ b/platform-enterprise_versioned_docs/version-22.4/secrets/overview.md @@ -38,7 +38,7 @@ Secrets defined by a user have higher priority and will override any Secrets def ### Using Secrets in workflows -When a new workflow is launched, all Secrets are sent to the corresponding secret manager for the Compute Environment. Nextflow will download these Secrets internally and use them when they are referenced in the pipeline code as described in the [Nextflow Secrets documentation](https://www.nextflow.io/docs/edge/secrets.html#process-secrets). +When a new workflow is launched, all Secrets are sent to the corresponding secret manager for the Compute Environment. Nextflow will download these Secrets internally and use them when they are referenced in the pipeline code as described in the [Nextflow Secrets documentation](https://docs.seqera.io/nextflow/secrets). Secrets will be automatically deleted from the secret manager when the Pipeline completes (successful or unsuccessful). diff --git a/platform-enterprise_versioned_docs/version-22.4/supported_software/dragen/overview.md b/platform-enterprise_versioned_docs/version-22.4/supported_software/dragen/overview.md index ac78895c6..d88514f2f 100644 --- a/platform-enterprise_versioned_docs/version-22.4/supported_software/dragen/overview.md +++ b/platform-enterprise_versioned_docs/version-22.4/supported_software/dragen/overview.md @@ -60,7 +60,7 @@ Please see the [dragen.nf](https://github.com/seqeralabs/nf-dragen/blob/master/m } ``` - Please refer to the [Nextflow label docs](https://www.nextflow.io/docs/latest/process.html?highlight=label#label) for more information. + Please refer to the [Nextflow label docs](https://docs.seqera.io/nextflow/process.html?highlight=label#label) for more information. 2. Define Secrets diff --git a/platform-enterprise_versioned_docs/version-22.4/supported_software/fusion/fusion.md b/platform-enterprise_versioned_docs/version-22.4/supported_software/fusion/fusion.md index 8c9c6fa32..d2c629668 100644 --- a/platform-enterprise_versioned_docs/version-22.4/supported_software/fusion/fusion.md +++ b/platform-enterprise_versioned_docs/version-22.4/supported_software/fusion/fusion.md @@ -15,7 +15,7 @@ To enable Fusion in Tower: - Use Nextflow version `22.10.0` or later. The latest version of Nextflow is used in Tower by default, but a particular version can be specified using `NXF_VER` in the Nextflow config file field (**Advanced options -> Nextflow config file** under Pipeline settings on the launch page). -- Enable the [Wave containers service](https://www.nextflow.io/docs/latest/wave.html#wave-page) during [AWS Batch](../../compute-envs/aws-batch) compute environment creation. +- Enable the [Wave containers service](https://docs.seqera.io/nextflow/wave#wave-page) during [AWS Batch](../../compute-envs/aws-batch) compute environment creation. - Select **Enable Fusion v2** during compute environment creation. diff --git a/platform-enterprise_versioned_docs/version-23.1/compute-envs/altair-grid-engine.md b/platform-enterprise_versioned_docs/version-23.1/compute-envs/altair-grid-engine.md index 90be5fa89..a746ca161 100644 --- a/platform-enterprise_versioned_docs/version-23.1/compute-envs/altair-grid-engine.md +++ b/platform-enterprise_versioned_docs/version-23.1/compute-envs/altair-grid-engine.md @@ -15,7 +15,7 @@ To launch pipelines into a **Grid Engine** cluster from Tower, the following req - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Compute environment @@ -42,7 +42,7 @@ To create a new compute environment for **Grid Engine** in Tower: 10. Enter the **Compute queue name**. This is the cluster queue to which the Nextflow job will submit tasks. :::tip - The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://www.nextflow.io/docs/latest/process.html#queue) for more details. + The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. Expand **Staging options** to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment. diff --git a/platform-enterprise_versioned_docs/version-23.1/compute-envs/altair-pbs-pro.md b/platform-enterprise_versioned_docs/version-23.1/compute-envs/altair-pbs-pro.md index d52c2866d..a76213cae 100644 --- a/platform-enterprise_versioned_docs/version-23.1/compute-envs/altair-pbs-pro.md +++ b/platform-enterprise_versioned_docs/version-23.1/compute-envs/altair-pbs-pro.md @@ -15,7 +15,7 @@ To launch pipelines into a **PBS Pro** cluster from Tower, the following require - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Compute environment @@ -42,7 +42,7 @@ To create a new compute environment for **PBS Pro** in Tower: 10. Enter the **Compute queue name**. This is the cluster queue to which the Nextflow job will submit tasks. :::tip - The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://www.nextflow.io/docs/latest/process.html#queue) for more details. + The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. Expand **Staging options** to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment. diff --git a/platform-enterprise_versioned_docs/version-23.1/compute-envs/aws-batch.md b/platform-enterprise_versioned_docs/version-23.1/compute-envs/aws-batch.md index 32d8003e5..74028c71a 100644 --- a/platform-enterprise_versioned_docs/version-23.1/compute-envs/aws-batch.md +++ b/platform-enterprise_versioned_docs/version-23.1/compute-envs/aws-batch.md @@ -127,7 +127,7 @@ Once the AWS resources are set up, we can add a new **AWS Batch** environment in The bucket should be in the same region selected in the previous step. ::: -9. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +9. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 10. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled (see above). See [Fusion file system](../supported_software/fusion/overview) for configuration details. diff --git a/platform-enterprise_versioned_docs/version-23.1/compute-envs/azure-batch.md b/platform-enterprise_versioned_docs/version-23.1/compute-envs/azure-batch.md index 4f7c50128..080a9b94f 100644 --- a/platform-enterprise_versioned_docs/version-23.1/compute-envs/azure-batch.md +++ b/platform-enterprise_versioned_docs/version-23.1/compute-envs/azure-batch.md @@ -122,7 +122,7 @@ Once the Azure resources are set up, add a new compute environment in Tower: 13. Enable **Dispose resources** if you'd like Tower to automatically delete the Batch pool once the workflow is complete. -14. Select or create a [**Container registry credential**](../credentials/azure_registry_credentials) to authenticate to an Azure registry (used by the [Wave containers](https://www.nextflow.io/docs/latest/wave.html) service). +14. Select or create a [**Container registry credential**](../credentials/azure_registry_credentials) to authenticate to an Azure registry (used by the [Wave containers](https://docs.seqera.io/nextflow/wave) service). 15. Apply [**Resource labels**](../resource-labels/overview) to the cloud resources consumed by this compute environment. Workspace default resource labels are prefilled. diff --git a/platform-enterprise_versioned_docs/version-23.1/compute-envs/google-cloud-batch.md b/platform-enterprise_versioned_docs/version-23.1/compute-envs/google-cloud-batch.md index f0fade44c..d9ac1bc3f 100644 --- a/platform-enterprise_versioned_docs/version-23.1/compute-envs/google-cloud-batch.md +++ b/platform-enterprise_versioned_docs/version-23.1/compute-envs/google-cloud-batch.md @@ -126,7 +126,7 @@ To create a new compute environment for Google Cloud in Tower: 8. In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket should be accessible in the location selected in the previous step. -9. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +9. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 10. Select **Enable Fusion v2** to allow access to your GCS-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled (see above). diff --git a/platform-enterprise_versioned_docs/version-23.1/compute-envs/hpc.md b/platform-enterprise_versioned_docs/version-23.1/compute-envs/hpc.md index 1eac5295d..68431ac9b 100644 --- a/platform-enterprise_versioned_docs/version-23.1/compute-envs/hpc.md +++ b/platform-enterprise_versioned_docs/version-23.1/compute-envs/hpc.md @@ -19,7 +19,7 @@ To launch pipelines into an **HPC** cluster from Tower, the following requiremen - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Compute environment @@ -41,9 +41,9 @@ To create a new **HPC** compute environment in Tower: 8. Enter the **Login hostname**. This is usually the hostname or public IP address of the cluster's login node. -9. Enter the **Head queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will be submitted. +9. Enter the **Head queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will be submitted. -10. Enter the **Compute queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will submit tasks. +10. Enter the **Compute queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will submit tasks. 11. Expand **Staging options** to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment. diff --git a/platform-enterprise_versioned_docs/version-23.1/compute-envs/lsf.md b/platform-enterprise_versioned_docs/version-23.1/compute-envs/lsf.md index 0251e20f5..43b790c60 100644 --- a/platform-enterprise_versioned_docs/version-23.1/compute-envs/lsf.md +++ b/platform-enterprise_versioned_docs/version-23.1/compute-envs/lsf.md @@ -15,7 +15,7 @@ To launch pipelines into an **LSF** cluster from Tower, the following requiremen - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Compute environment @@ -42,7 +42,7 @@ To create a new compute environment for **LSF** in Tower: 10. Enter the **Compute queue name**. This is the cluster queue to which the Nextflow job will submit tasks. :::tip - The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://www.nextflow.io/docs/latest/process.html#queue) for more details. + The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. Expand **Staging options** to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment. diff --git a/platform-enterprise_versioned_docs/version-23.1/compute-envs/moab.md b/platform-enterprise_versioned_docs/version-23.1/compute-envs/moab.md index 03dc79354..7629cbbbe 100644 --- a/platform-enterprise_versioned_docs/version-23.1/compute-envs/moab.md +++ b/platform-enterprise_versioned_docs/version-23.1/compute-envs/moab.md @@ -15,7 +15,7 @@ To launch pipelines into a **Moab** cluster from Tower, the following requiremen - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Compute environment @@ -42,7 +42,7 @@ To create a new compute environment for **Moab** in Tower: 10. Enter the **Compute queue name**. This is the cluster queue to which the Nextflow job will submit tasks. :::tip - The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://www.nextflow.io/docs/latest/process.html#queue) for more details. + The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. Expand **Staging options** to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment. diff --git a/platform-enterprise_versioned_docs/version-23.1/compute-envs/overview.md b/platform-enterprise_versioned_docs/version-23.1/compute-envs/overview.md index 031e32a57..84e88c506 100644 --- a/platform-enterprise_versioned_docs/version-23.1/compute-envs/overview.md +++ b/platform-enterprise_versioned_docs/version-23.1/compute-envs/overview.md @@ -48,7 +48,7 @@ The AWS Batch compute environment creation form in Tower includes an **Enable GP - This setting can be overridden by **AMI ID** in the advanced options. -- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: +- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://docs.seqera.io/nextflow/process#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: ```groovy process { diff --git a/platform-enterprise_versioned_docs/version-23.1/compute-envs/slurm.md b/platform-enterprise_versioned_docs/version-23.1/compute-envs/slurm.md index 49eb2dbdc..6ddac5d5e 100644 --- a/platform-enterprise_versioned_docs/version-23.1/compute-envs/slurm.md +++ b/platform-enterprise_versioned_docs/version-23.1/compute-envs/slurm.md @@ -15,7 +15,7 @@ To launch pipelines into a **Slurm** cluster from Tower, the following requireme - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Compute environment @@ -42,7 +42,7 @@ To create a new compute environment for **Slurm** in Tower: 10. Enter the **Compute queue name**. This is the cluster queue to which the Nextflow job will submit tasks. :::tip - The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://www.nextflow.io/docs/latest/process.html#queue) for more details. + The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. Expand **Staging options** to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment. diff --git a/platform-enterprise_versioned_docs/version-23.1/credentials/aws_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.1/credentials/aws_registry_credentials.md index 18a8c5ebf..ac937d499 100644 --- a/platform-enterprise_versioned_docs/version-23.1/credentials/aws_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.1/credentials/aws_registry_credentials.md @@ -7,7 +7,7 @@ tags: [aws, ecr, credentials] ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-23.1/credentials/azure_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.1/credentials/azure_registry_credentials.md index 204d0e629..ddeff8520 100644 --- a/platform-enterprise_versioned_docs/version-23.1/credentials/azure_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.1/credentials/azure_registry_credentials.md @@ -7,7 +7,7 @@ tags: [azure, registry, credentials] ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-23.1/credentials/docker_hub_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.1/credentials/docker_hub_registry_credentials.md index 37a03a5a4..6f86f4c01 100644 --- a/platform-enterprise_versioned_docs/version-23.1/credentials/docker_hub_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.1/credentials/docker_hub_registry_credentials.md @@ -7,7 +7,7 @@ tags: [docker, registry, credentials] ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-23.1/credentials/google_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.1/credentials/google_registry_credentials.md index 21936e35b..cff89f88d 100644 --- a/platform-enterprise_versioned_docs/version-23.1/credentials/google_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.1/credentials/google_registry_credentials.md @@ -7,7 +7,7 @@ tags: [google, container, registry, artifact, credentials] ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-23.1/credentials/quay_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.1/credentials/quay_registry_credentials.md index 28308c1b4..53de54c97 100644 --- a/platform-enterprise_versioned_docs/version-23.1/credentials/quay_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.1/credentials/quay_registry_credentials.md @@ -7,7 +7,7 @@ tags: [quay, credentials] ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-23.1/enterprise/configuration/wave.md b/platform-enterprise_versioned_docs/version-23.1/enterprise/configuration/wave.md index 53f94ce98..9bc6efc06 100644 --- a/platform-enterprise_versioned_docs/version-23.1/enterprise/configuration/wave.md +++ b/platform-enterprise_versioned_docs/version-23.1/enterprise/configuration/wave.md @@ -7,7 +7,7 @@ tags: [wave, containers, configuration] From version 22.4, Tower supports Seqera Labs' Wave containers service for on-premise installations. -Learn more about Wave's features [here](https://wave.seqera.io), and about Wave integration with Nextflow [here](https://www.nextflow.io/docs/latest/wave.html). +Learn more about Wave's features [here](https://wave.seqera.io), and about Wave integration with Nextflow [here](https://docs.seqera.io/nextflow/wave). ## Pairing Tower with Wave @@ -37,4 +37,4 @@ When these conditions are met, the Wave feature is available on the Tower comput Once Wave is enabled, it will be possible to use private container repositories and the Fusion file system in your Nextflow pipelines. -Wave can also be enabled in the Nextflow pipeline config file. See [here](https://www.nextflow.io/docs/latest/wave.html) for more information. +Wave can also be enabled in the Nextflow pipeline config file. See [here](https://docs.seqera.io/nextflow/wave) for more information. diff --git a/platform-enterprise_versioned_docs/version-23.1/faqs.md b/platform-enterprise_versioned_docs/version-23.1/faqs.md index 20fe8054b..084c1b0e7 100644 --- a/platform-enterprise_versioned_docs/version-23.1/faqs.md +++ b/platform-enterprise_versioned_docs/version-23.1/faqs.md @@ -124,7 +124,7 @@ This error can occur if you execute a DSL 1-based Nextflow workflow using [Nextf The `sleep` commands within your Nextflow workflows may differ in behaviour depending on where they are: - If used within an `errorStrategy` block, the Groovy sleep function will be used (which takes its value in milliseconds). -- If used within a process script block, that language's sleep binary/method will be used. **Example:** [this BASH script](https://www.nextflow.io/docs/latest/metrics.html?highlight=sleep) uses the BASH sleep binary, which takes its value in seconds. +- If used within a process script block, that language's sleep binary/method will be used. **Example:** [this BASH script](https://docs.seqera.io/nextflow/metrics.html?highlight=sleep) uses the BASH sleep binary, which takes its value in seconds. **

Q: Why does re-launching/resuming a run fail with `field revision is not writable`?

** @@ -414,7 +414,7 @@ To resolve the issue, please try reloading the UI to reinitiate the client's con **

Q: How can I specify Nextflow CLI run arguments when launching from Tower?

** -As of Nextflow v22.09.1-edge, when invoking a pipeline from Tower, you can specify [Nextflow CLI run arguments](https://www.nextflow.io/docs/latest/cli.html?highlight=dump#run) by setting the `NXF_CLI_OPTS` environment variable via pre-run script: +As of Nextflow v22.09.1-edge, when invoking a pipeline from Tower, you can specify [Nextflow CLI run arguments](https://docs.seqera.io/nextflow/cli.html?highlight=dump#run) by setting the `NXF_CLI_OPTS` environment variable via pre-run script: ``` # Example: @@ -443,7 +443,7 @@ Current as of May 16, 2022, there is no solution for this problem other than to **

Q: Is it possible to maintain different Nextflow configuration files for different environments?

** -Yes. The main `nextflow.config` file will always be imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [their own profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) in the main `nextflow.config`. +Yes. The main `nextflow.config` file will always be imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [their own profile](https://docs.seqera.io/nextflow/config#config-profiles) in the main `nextflow.config`. Example: @@ -555,7 +555,7 @@ process.afterScript = 'sleep 60' **

Q: Why are jobs in RUNNING status not terminated when my pipeline run is canceled?

** -The behavior of Tower when canceling a run depends on the [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: +The behavior of Tower when canceling a run depends on the [`errorStrategy`](https://docs.seqera.io/nextflow/process#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: ```bash @@ -602,7 +602,7 @@ The Groovy shell used by Nextflow to execute your workflow has a hard limit on s 1. Remove any unnecessary code or comments from the script. 2. Move long script bodies into a separate script file in the pipeline `/bin` directory. -3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://www.nextflow.io/docs/latest/dsl2.html#modules). +3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://docs.seqera.io/nextflow/dsl2#modules). ## Nextflow Launcher @@ -812,7 +812,7 @@ Note: 1. Activation does not cause GPU-enabled instances to automatically spawn in your Batch cluster. You must still specify these in the Forge screen's **Advanced options > Instance types** field. 2. Population of the Forge screen's **Advanced options > AMI Id** field will supersede the AWS-recommended AMI. -3. Your Nextflow script must include [accelerator directives](https://www.nextflow.io/docs/latest/process.html?highlight=accelerator) to use the provisioned GPUs. +3. Your Nextflow script must include [accelerator directives](https://docs.seqera.io/nextflow/process.html?highlight=accelerator) to use the provisioned GPUs. ## tw CLI diff --git a/platform-enterprise_versioned_docs/version-23.1/getting-started/deployment-options.md b/platform-enterprise_versioned_docs/version-23.1/getting-started/deployment-options.md index fdf40e406..a73d06f2e 100644 --- a/platform-enterprise_versioned_docs/version-23.1/getting-started/deployment-options.md +++ b/platform-enterprise_versioned_docs/version-23.1/getting-started/deployment-options.md @@ -103,5 +103,5 @@ Bearer token support requires Nextflow version 20.10.0 or later. Set with the `N To configure and execute Nextflow pipelines in cloud environments, see [compute environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-enterprise_versioned_docs/version-23.1/getting-started/usage.md b/platform-enterprise_versioned_docs/version-23.1/getting-started/usage.md index 0b4f94f3c..becfd00f1 100644 --- a/platform-enterprise_versioned_docs/version-23.1/getting-started/usage.md +++ b/platform-enterprise_versioned_docs/version-23.1/getting-started/usage.md @@ -75,5 +75,5 @@ The workspace ID can be found on the organization workspaces overview page. To configure and execute Nextflow pipelines in cloud environments, see [Compute Environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-enterprise_versioned_docs/version-23.1/launch/advanced.md b/platform-enterprise_versioned_docs/version-23.1/launch/advanced.md index 55627fa2f..681e0da4d 100644 --- a/platform-enterprise_versioned_docs/version-23.1/launch/advanced.md +++ b/platform-enterprise_versioned_docs/version-23.1/launch/advanced.md @@ -11,7 +11,7 @@ Advanced launch options allow users to modify the configuration and execution of The _Nextflow config_ field allows the addition of settings to the Nextflow configuration file. -This text should follow the same syntax as the [Nextflow configuration file](https://www.nextflow.io/docs/latest/config.html#config-syntax). +This text should follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax). In the example below, we can modify the **manifest** section to give the pipeline a name and description which will show up in the Tower monitoring section. diff --git a/platform-enterprise_versioned_docs/version-23.1/launch/launch-form.md b/platform-enterprise_versioned_docs/version-23.1/launch/launch-form.md index 27266cd55..52c40efd5 100644 --- a/platform-enterprise_versioned_docs/version-23.1/launch/launch-form.md +++ b/platform-enterprise_versioned_docs/version-23.1/launch/launch-form.md @@ -20,7 +20,7 @@ To launch a pipeline: 3. Enter a repository URL for the **Pipeline to launch** (e.g. `https://github.com/nf-core/rnaseq.git`). :::tip -Nextflow pipelines are just Git repositories and they can reside on any public or private Git-hosting platform. See [Git Integration](../git/overview) in the Tower docs and [Pipeline Sharing](https://www.nextflow.io/docs/latest/sharing.html) in the Nextflow docs for more details. +Nextflow pipelines are just Git repositories and they can reside on any public or private Git-hosting platform. See [Git Integration](../git/overview) in the Tower docs and [Pipeline Sharing](https://docs.seqera.io/nextflow/sharing) in the Nextflow docs for more details. ::: 4. You can select a **Revision number** to use a specific version of the pipeline. @@ -37,7 +37,7 @@ The credentials associated with the compute environment must be able to access t 6. Select any **Config profiles** you would like to use. - Visit the Nextflow [Config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) documentation for more details. + Visit the Nextflow [Config profiles](https://docs.seqera.io/nextflow/config#config-profiles) documentation for more details. 7. Enter any **Pipeline parameters** in YAML or JSON format. diff --git a/platform-enterprise_versioned_docs/version-23.1/secrets/overview.md b/platform-enterprise_versioned_docs/version-23.1/secrets/overview.md index 27b1acef2..0ceca80ed 100644 --- a/platform-enterprise_versioned_docs/version-23.1/secrets/overview.md +++ b/platform-enterprise_versioned_docs/version-23.1/secrets/overview.md @@ -39,7 +39,7 @@ Secrets defined by a user have higher priority and will override any Secrets def ### Using Secrets in workflows -When a new workflow is launched, all Secrets are sent to the corresponding secret manager for the Compute Environment. Nextflow will download these Secrets internally and use them when they are referenced in the pipeline code as described in the [Nextflow Secrets documentation](https://www.nextflow.io/docs/edge/secrets.html#process-secrets). +When a new workflow is launched, all Secrets are sent to the corresponding secret manager for the Compute Environment. Nextflow will download these Secrets internally and use them when they are referenced in the pipeline code as described in the [Nextflow Secrets documentation](https://docs.seqera.io/nextflow/secrets). Secrets will be automatically deleted from the secret manager when the Pipeline completes (successful or unsuccessful). diff --git a/platform-enterprise_versioned_docs/version-23.1/supported_software/dragen/overview.md b/platform-enterprise_versioned_docs/version-23.1/supported_software/dragen/overview.md index 98503fec5..ed61bdd4a 100644 --- a/platform-enterprise_versioned_docs/version-23.1/supported_software/dragen/overview.md +++ b/platform-enterprise_versioned_docs/version-23.1/supported_software/dragen/overview.md @@ -61,7 +61,7 @@ Please see the [dragen.nf](https://github.com/seqeralabs/nf-dragen/blob/master/m } ``` - Please refer to the [Nextflow label docs](https://www.nextflow.io/docs/latest/process.html?highlight=label#label) for more information. + Please refer to the [Nextflow label docs](https://docs.seqera.io/nextflow/process.html?highlight=label#label) for more information. 2. Define Secrets diff --git a/platform-enterprise_versioned_docs/version-23.2/compute-envs/altair-grid-engine.md b/platform-enterprise_versioned_docs/version-23.2/compute-envs/altair-grid-engine.md index 809924ffb..062800b03 100644 --- a/platform-enterprise_versioned_docs/version-23.2/compute-envs/altair-grid-engine.md +++ b/platform-enterprise_versioned_docs/version-23.2/compute-envs/altair-grid-engine.md @@ -15,7 +15,7 @@ To launch pipelines into a **Grid Engine** cluster from Tower, the following req - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Compute environment @@ -42,7 +42,7 @@ To create a new compute environment for **Grid Engine** in Tower: 10. Enter the **Compute queue name**. This is the cluster queue to which the Nextflow job will submit tasks. :::tip -The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://www.nextflow.io/docs/latest/process.html#queue) for more details. +The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. Expand **Staging options** to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment. diff --git a/platform-enterprise_versioned_docs/version-23.2/compute-envs/altair-pbs-pro.md b/platform-enterprise_versioned_docs/version-23.2/compute-envs/altair-pbs-pro.md index 52fb69710..2094f51c0 100644 --- a/platform-enterprise_versioned_docs/version-23.2/compute-envs/altair-pbs-pro.md +++ b/platform-enterprise_versioned_docs/version-23.2/compute-envs/altair-pbs-pro.md @@ -15,7 +15,7 @@ To launch pipelines into a **PBS Pro** cluster from Tower, the following require - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Compute environment @@ -42,7 +42,7 @@ To create a new compute environment for **PBS Pro** in Tower: 10. Enter the **Compute queue name**. This is the cluster queue to which the Nextflow job will submit tasks. :::tip -The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://www.nextflow.io/docs/latest/process.html#queue) for more details. +The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. Expand **Staging options** to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment. diff --git a/platform-enterprise_versioned_docs/version-23.2/compute-envs/aws-batch.md b/platform-enterprise_versioned_docs/version-23.2/compute-envs/aws-batch.md index 56e64f3b4..dd2825b39 100644 --- a/platform-enterprise_versioned_docs/version-23.2/compute-envs/aws-batch.md +++ b/platform-enterprise_versioned_docs/version-23.2/compute-envs/aws-batch.md @@ -127,7 +127,7 @@ Once the AWS resources are set up, we can add a new **AWS Batch** environment in The bucket should be in the same region selected in the previous step. ::: -9. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +9. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 10. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled (see above). See [Fusion file system](../supported_software/fusion/overview) for configuration details. diff --git a/platform-enterprise_versioned_docs/version-23.2/compute-envs/azure-batch.md b/platform-enterprise_versioned_docs/version-23.2/compute-envs/azure-batch.md index 16096b5a8..ae0397d5c 100644 --- a/platform-enterprise_versioned_docs/version-23.2/compute-envs/azure-batch.md +++ b/platform-enterprise_versioned_docs/version-23.2/compute-envs/azure-batch.md @@ -122,7 +122,7 @@ The blob container must be in the same **Region** from step 7. 13. Enable **Dispose resources** if you'd like Tower to automatically delete the Batch pool once the workflow is complete. -14. Select or create a [**Container registry credential**](../credentials/azure_registry_credentials) to authenticate to an Azure registry (used by the [Wave containers](https://www.nextflow.io/docs/latest/wave.html) service). +14. Select or create a [**Container registry credential**](../credentials/azure_registry_credentials) to authenticate to an Azure registry (used by the [Wave containers](https://docs.seqera.io/nextflow/wave) service). 15. Apply [**Resource labels**](../resource-labels/overview) to the cloud resources consumed by this compute environment. Workspace default resource labels are prefilled. diff --git a/platform-enterprise_versioned_docs/version-23.2/compute-envs/google-cloud-batch.md b/platform-enterprise_versioned_docs/version-23.2/compute-envs/google-cloud-batch.md index 2704d9fbd..52684a501 100644 --- a/platform-enterprise_versioned_docs/version-23.2/compute-envs/google-cloud-batch.md +++ b/platform-enterprise_versioned_docs/version-23.2/compute-envs/google-cloud-batch.md @@ -126,7 +126,7 @@ To create a new compute environment for Google Cloud in Tower: 8. In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket should be accessible in the location selected in the previous step. -9. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +9. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 10. Select **Enable Fusion v2** to allow access to your GCS-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled (see above). diff --git a/platform-enterprise_versioned_docs/version-23.2/compute-envs/hpc.md b/platform-enterprise_versioned_docs/version-23.2/compute-envs/hpc.md index 1eac5295d..68431ac9b 100644 --- a/platform-enterprise_versioned_docs/version-23.2/compute-envs/hpc.md +++ b/platform-enterprise_versioned_docs/version-23.2/compute-envs/hpc.md @@ -19,7 +19,7 @@ To launch pipelines into an **HPC** cluster from Tower, the following requiremen - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Compute environment @@ -41,9 +41,9 @@ To create a new **HPC** compute environment in Tower: 8. Enter the **Login hostname**. This is usually the hostname or public IP address of the cluster's login node. -9. Enter the **Head queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will be submitted. +9. Enter the **Head queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will be submitted. -10. Enter the **Compute queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will submit tasks. +10. Enter the **Compute queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will submit tasks. 11. Expand **Staging options** to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment. diff --git a/platform-enterprise_versioned_docs/version-23.2/compute-envs/lsf.md b/platform-enterprise_versioned_docs/version-23.2/compute-envs/lsf.md index 1fb4d653a..9172906b5 100644 --- a/platform-enterprise_versioned_docs/version-23.2/compute-envs/lsf.md +++ b/platform-enterprise_versioned_docs/version-23.2/compute-envs/lsf.md @@ -15,7 +15,7 @@ To launch pipelines into an **LSF** cluster from Tower, the following requiremen - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Compute environment @@ -42,7 +42,7 @@ To create a new compute environment for **LSF** in Tower: 10. Enter the **Compute queue name**. This is the cluster queue to which the Nextflow job will submit tasks. :::tip -The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://www.nextflow.io/docs/latest/process.html#queue) for more details. +The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. Expand **Staging options** to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment. diff --git a/platform-enterprise_versioned_docs/version-23.2/compute-envs/moab.md b/platform-enterprise_versioned_docs/version-23.2/compute-envs/moab.md index 5849c88a8..ab2e6e0c7 100644 --- a/platform-enterprise_versioned_docs/version-23.2/compute-envs/moab.md +++ b/platform-enterprise_versioned_docs/version-23.2/compute-envs/moab.md @@ -15,7 +15,7 @@ To launch pipelines into a **Moab** cluster from Tower, the following requiremen - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Compute environment @@ -42,7 +42,7 @@ To create a new compute environment for **Moab** in Tower: 10. Enter the **Compute queue name**. This is the cluster queue to which the Nextflow job will submit tasks. :::tip -The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://www.nextflow.io/docs/latest/process.html#queue) for more details. +The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. Expand **Staging options** to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment. diff --git a/platform-enterprise_versioned_docs/version-23.2/compute-envs/overview.md b/platform-enterprise_versioned_docs/version-23.2/compute-envs/overview.md index b595f6cb9..092d48797 100644 --- a/platform-enterprise_versioned_docs/version-23.2/compute-envs/overview.md +++ b/platform-enterprise_versioned_docs/version-23.2/compute-envs/overview.md @@ -48,7 +48,7 @@ The AWS Batch compute environment creation form in Tower includes an **Enable GP - This setting can be overridden by **AMI ID** in the advanced options. -- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. For example: +- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://docs.seqera.io/nextflow/process#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. For example: ```groovy process UseGPU { diff --git a/platform-enterprise_versioned_docs/version-23.2/compute-envs/slurm.md b/platform-enterprise_versioned_docs/version-23.2/compute-envs/slurm.md index 494a538c7..569babb05 100644 --- a/platform-enterprise_versioned_docs/version-23.2/compute-envs/slurm.md +++ b/platform-enterprise_versioned_docs/version-23.2/compute-envs/slurm.md @@ -15,7 +15,7 @@ To launch pipelines into a **Slurm** cluster from Tower, the following requireme - The cluster should allow outbound connections to the Tower web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Compute environment @@ -42,7 +42,7 @@ To create a new compute environment for **Slurm** in Tower: 10. Enter the **Compute queue name**. This is the cluster queue to which the Nextflow job will submit tasks. :::tip -The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://www.nextflow.io/docs/latest/process.html#queue) for more details. +The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow [documentation](https://docs.seqera.io/nextflow/process#queue) for more details. ::: 11. Expand **Staging options** to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment. diff --git a/platform-enterprise_versioned_docs/version-23.2/credentials/aws_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.2/credentials/aws_registry_credentials.md index 5851f50bc..bb76a26cd 100644 --- a/platform-enterprise_versioned_docs/version-23.2/credentials/aws_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.2/credentials/aws_registry_credentials.md @@ -7,7 +7,7 @@ tags: [aws, ecr, credentials] ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-23.2/credentials/azure_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.2/credentials/azure_registry_credentials.md index 204d0e629..ddeff8520 100644 --- a/platform-enterprise_versioned_docs/version-23.2/credentials/azure_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.2/credentials/azure_registry_credentials.md @@ -7,7 +7,7 @@ tags: [azure, registry, credentials] ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-23.2/credentials/docker_hub_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.2/credentials/docker_hub_registry_credentials.md index 37a03a5a4..6f86f4c01 100644 --- a/platform-enterprise_versioned_docs/version-23.2/credentials/docker_hub_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.2/credentials/docker_hub_registry_credentials.md @@ -7,7 +7,7 @@ tags: [docker, registry, credentials] ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-23.2/credentials/google_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.2/credentials/google_registry_credentials.md index 21936e35b..cff89f88d 100644 --- a/platform-enterprise_versioned_docs/version-23.2/credentials/google_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.2/credentials/google_registry_credentials.md @@ -7,7 +7,7 @@ tags: [google, container, registry, artifact, credentials] ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-23.2/credentials/quay_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.2/credentials/quay_registry_credentials.md index 28308c1b4..53de54c97 100644 --- a/platform-enterprise_versioned_docs/version-23.2/credentials/quay_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.2/credentials/quay_registry_credentials.md @@ -7,7 +7,7 @@ tags: [quay, credentials] ## Container registry credentials -From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Tower supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [here](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only leveraged by the Wave containers service. In order for your pipeline execution to leverage Wave containers, add `wave { enabled=true }` either to the **Nextflow config** field on the launch page, or to your nextflow.config file. diff --git a/platform-enterprise_versioned_docs/version-23.2/enterprise/configuration/wave.md b/platform-enterprise_versioned_docs/version-23.2/enterprise/configuration/wave.md index 85bcd6580..84468cba7 100644 --- a/platform-enterprise_versioned_docs/version-23.2/enterprise/configuration/wave.md +++ b/platform-enterprise_versioned_docs/version-23.2/enterprise/configuration/wave.md @@ -7,7 +7,7 @@ tags: [wave, containers, configuration] From version 22.4, Tower supports Seqera Labs' Wave containers service for on-premise installations. -Learn more about Wave's features [here](https://wave.seqera.io), and about Wave integration with Nextflow [here](https://www.nextflow.io/docs/latest/wave.html). +Learn more about Wave's features [here](https://wave.seqera.io), and about Wave integration with Nextflow [here](https://docs.seqera.io/nextflow/wave). ## Pairing Tower with Wave @@ -37,4 +37,4 @@ When these conditions are met, the Wave feature is available on the Tower comput Once Wave is enabled, it will be possible to use private container repositories and the Fusion file system in your Nextflow pipelines. -Wave can also be enabled in the Nextflow pipeline config file. See [here](https://www.nextflow.io/docs/latest/wave.html) for more information. +Wave can also be enabled in the Nextflow pipeline config file. See [here](https://docs.seqera.io/nextflow/wave) for more information. diff --git a/platform-enterprise_versioned_docs/version-23.2/faqs.md b/platform-enterprise_versioned_docs/version-23.2/faqs.md index f19d16298..90545444c 100644 --- a/platform-enterprise_versioned_docs/version-23.2/faqs.md +++ b/platform-enterprise_versioned_docs/version-23.2/faqs.md @@ -124,7 +124,7 @@ This error can occur if you execute a DSL 1-based Nextflow workflow using [Nextf The `sleep` commands within your Nextflow workflows may differ in behaviour depending on where they are: - If used within an `errorStrategy` block, the Groovy sleep function will be used (which takes its value in milliseconds). -- If used within a process script block, that language's sleep binary/method will be used. **Example:** [this BASH script](https://www.nextflow.io/docs/latest/metrics.html?highlight=sleep) uses the BASH sleep binary, which takes its value in seconds. +- If used within a process script block, that language's sleep binary/method will be used. **Example:** [this BASH script](https://docs.seqera.io/nextflow/metrics.html?highlight=sleep) uses the BASH sleep binary, which takes its value in seconds. **

Q: Why does relaunching/resuming a run fail with `field revision is not writable`?

** @@ -414,7 +414,7 @@ To resolve the issue, please try reloading the UI to reinitiate the client's con **

Q: How can I specify Nextflow CLI run arguments when launching from Tower?

** -As of Nextflow v22.09.1-edge, when invoking a pipeline from Tower, you can specify [Nextflow CLI run arguments](https://www.nextflow.io/docs/latest/cli.html?highlight=dump#run) by setting the `NXF_CLI_OPTS` environment variable via pre-run script: +As of Nextflow v22.09.1-edge, when invoking a pipeline from Tower, you can specify [Nextflow CLI run arguments](https://docs.seqera.io/nextflow/cli.html?highlight=dump#run) by setting the `NXF_CLI_OPTS` environment variable via pre-run script: ``` # Example: @@ -443,7 +443,7 @@ Current as of May 16, 2022, there is no solution for this problem other than to **

Q: Is it possible to maintain different Nextflow configuration files for different environments?

** -Yes. The main `nextflow.config` file will always be imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [their own profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) in the main `nextflow.config`. +Yes. The main `nextflow.config` file will always be imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [their own profile](https://docs.seqera.io/nextflow/config#config-profiles) in the main `nextflow.config`. Example: @@ -555,7 +555,7 @@ process.afterScript = 'sleep 60' **

Q: Why are jobs in RUNNING status not terminated when my pipeline run is canceled?

** -The behavior of Tower when canceling a run depends on the [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: +The behavior of Tower when canceling a run depends on the [`errorStrategy`](https://docs.seqera.io/nextflow/process#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: ```bash @@ -602,7 +602,7 @@ The Groovy shell used by Nextflow to execute your workflow has a hard limit on s 1. Remove any unnecessary code or comments from the script. 2. Move long script bodies into a separate script file in the pipeline `/bin` directory. -3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://www.nextflow.io/docs/latest/dsl2.html#modules). +3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://docs.seqera.io/nextflow/dsl2#modules). ## Nextflow Launcher @@ -812,7 +812,7 @@ Note: 1. Activation does not cause GPU-enabled instances to automatically spawn in your Batch cluster. You must still specify these in the Forge screen's **Advanced options > Instance types** field. 2. Population of the Forge screen's **Advanced options > AMI Id** field will supersede the AWS-recommended AMI. -3. Your Nextflow script must include [accelerator directives](https://www.nextflow.io/docs/latest/process.html?highlight=accelerator) to use the provisioned GPUs. +3. Your Nextflow script must include [accelerator directives](https://docs.seqera.io/nextflow/process.html?highlight=accelerator) to use the provisioned GPUs. ## tw CLI diff --git a/platform-enterprise_versioned_docs/version-23.2/getting-started/deployment-options.md b/platform-enterprise_versioned_docs/version-23.2/getting-started/deployment-options.md index 7f34353d5..6e0d940b4 100644 --- a/platform-enterprise_versioned_docs/version-23.2/getting-started/deployment-options.md +++ b/platform-enterprise_versioned_docs/version-23.2/getting-started/deployment-options.md @@ -107,5 +107,5 @@ Bearer token support requires Nextflow version 20.10.0 or later. Set with the `N To configure and execute Nextflow pipelines in cloud environments, see [compute environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-enterprise_versioned_docs/version-23.2/getting-started/usage.md b/platform-enterprise_versioned_docs/version-23.2/getting-started/usage.md index 33072d556..0982acebd 100644 --- a/platform-enterprise_versioned_docs/version-23.2/getting-started/usage.md +++ b/platform-enterprise_versioned_docs/version-23.2/getting-started/usage.md @@ -75,5 +75,5 @@ The workspace ID can be found on the organization workspaces overview page. To configure and execute Nextflow pipelines in cloud environments, see [Compute Environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-enterprise_versioned_docs/version-23.2/launch/advanced.md b/platform-enterprise_versioned_docs/version-23.2/launch/advanced.md index 55627fa2f..681e0da4d 100644 --- a/platform-enterprise_versioned_docs/version-23.2/launch/advanced.md +++ b/platform-enterprise_versioned_docs/version-23.2/launch/advanced.md @@ -11,7 +11,7 @@ Advanced launch options allow users to modify the configuration and execution of The _Nextflow config_ field allows the addition of settings to the Nextflow configuration file. -This text should follow the same syntax as the [Nextflow configuration file](https://www.nextflow.io/docs/latest/config.html#config-syntax). +This text should follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax). In the example below, we can modify the **manifest** section to give the pipeline a name and description which will show up in the Tower monitoring section. diff --git a/platform-enterprise_versioned_docs/version-23.2/launch/launch-form.md b/platform-enterprise_versioned_docs/version-23.2/launch/launch-form.md index 27266cd55..52c40efd5 100644 --- a/platform-enterprise_versioned_docs/version-23.2/launch/launch-form.md +++ b/platform-enterprise_versioned_docs/version-23.2/launch/launch-form.md @@ -20,7 +20,7 @@ To launch a pipeline: 3. Enter a repository URL for the **Pipeline to launch** (e.g. `https://github.com/nf-core/rnaseq.git`). :::tip -Nextflow pipelines are just Git repositories and they can reside on any public or private Git-hosting platform. See [Git Integration](../git/overview) in the Tower docs and [Pipeline Sharing](https://www.nextflow.io/docs/latest/sharing.html) in the Nextflow docs for more details. +Nextflow pipelines are just Git repositories and they can reside on any public or private Git-hosting platform. See [Git Integration](../git/overview) in the Tower docs and [Pipeline Sharing](https://docs.seqera.io/nextflow/sharing) in the Nextflow docs for more details. ::: 4. You can select a **Revision number** to use a specific version of the pipeline. @@ -37,7 +37,7 @@ The credentials associated with the compute environment must be able to access t 6. Select any **Config profiles** you would like to use. - Visit the Nextflow [Config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) documentation for more details. + Visit the Nextflow [Config profiles](https://docs.seqera.io/nextflow/config#config-profiles) documentation for more details. 7. Enter any **Pipeline parameters** in YAML or JSON format. diff --git a/platform-enterprise_versioned_docs/version-23.2/secrets/overview.md b/platform-enterprise_versioned_docs/version-23.2/secrets/overview.md index a7015ad69..49f4ee8c2 100644 --- a/platform-enterprise_versioned_docs/version-23.2/secrets/overview.md +++ b/platform-enterprise_versioned_docs/version-23.2/secrets/overview.md @@ -27,7 +27,7 @@ Secrets defined by a user have higher priority and will override any secrets wit ## Use secrets in workflows -When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally for use when referenced in the pipeline code. See [Nextflow secrets](https://www.nextflow.io/docs/edge/secrets.html#process-secrets) for more information. +When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally for use when referenced in the pipeline code. See [Nextflow secrets](https://docs.seqera.io/nextflow/secrets) for more information. Secrets will be automatically deleted from the secret manager when the pipeline completes, successfully or unsuccessfully. diff --git a/platform-enterprise_versioned_docs/version-23.2/supported_software/dragen/overview.md b/platform-enterprise_versioned_docs/version-23.2/supported_software/dragen/overview.md index b63fe8697..d76fa5ab7 100644 --- a/platform-enterprise_versioned_docs/version-23.2/supported_software/dragen/overview.md +++ b/platform-enterprise_versioned_docs/version-23.2/supported_software/dragen/overview.md @@ -59,7 +59,7 @@ Please see the [dragen.nf](https://github.com/seqeralabs/nf-dragen/blob/master/m } ``` - Please refer to the [Nextflow label docs](https://www.nextflow.io/docs/latest/process.html?highlight=label#label) for more information. + Please refer to the [Nextflow label docs](https://docs.seqera.io/nextflow/process.html?highlight=label#label) for more information. 2. Define Secrets diff --git a/platform-enterprise_versioned_docs/version-23.3/compute-envs/aws-batch.md b/platform-enterprise_versioned_docs/version-23.3/compute-envs/aws-batch.md index 3c98473cc..5d19ffc86 100644 --- a/platform-enterprise_versioned_docs/version-23.3/compute-envs/aws-batch.md +++ b/platform-enterprise_versioned_docs/version-23.3/compute-envs/aws-batch.md @@ -112,10 +112,10 @@ Batch Forge automatically creates resources that you may be charged for in your 9. Enter your S3 bucket path in the **Pipeline work directory** field, e.g., `s3://seqera-bucket`. This bucket must be in the same region chosen in the previous step. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: -10. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +10. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 11. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. When using Fusion v2 without fast instance storage (see below), the following EBS settings are applied to optimize file system performance: @@ -290,7 +290,7 @@ Your Seqera compute environment uses resources that you may be charged for in yo 8. Enter an S3 bucket path for the **Pipeline work directory**, e.g., `s3://seqera-bucket`. This bucket must be in the same region chosen in the previous step. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 9. Set the **Config mode** to **Manual**. diff --git a/platform-enterprise_versioned_docs/version-23.3/compute-envs/azure-batch.md b/platform-enterprise_versioned_docs/version-23.3/compute-envs/azure-batch.md index 785f6d982..252636ea0 100644 --- a/platform-enterprise_versioned_docs/version-23.3/compute-envs/azure-batch.md +++ b/platform-enterprise_versioned_docs/version-23.3/compute-envs/azure-batch.md @@ -146,7 +146,7 @@ You can create multiple credentials in your Seqera environment. 8. In the **Pipeline work directory** field, enter the Azure blob container created previously, e.g., `az://towerrgstorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 9. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. @@ -156,7 +156,7 @@ You can create multiple credentials in your Seqera environment. 13. Enter the **VMs count**. If autoscaling is enabled (default), this is the maximum number of VMs you wish the pool to scale up to. If autoscaling is disabled, this is the fixed number of virtual machines in the pool. 14. Enable **Autoscale** to scale up and down automatically, based on the number of pipeline tasks. The number of VMs will vary from **0** to **VMs count**. 15. Enable **Dispose resources** for Seqera to automatically delete the Batch pool if the compute environment is deleted on the platform. -16. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://www.nextflow.io/docs/latest/wave.html) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. +16. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://docs.seqera.io/nextflow/wave) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. 17. Apply [**Resource labels**](../resource-labels/overview). This will populate the **Metadata** fields of the Azure Batch pool. 18. Expand **Staging options** to include optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. 19. Specify custom **Environment variables** for the **Head job** and/or **Compute jobs**. @@ -194,7 +194,7 @@ You can create multiple credentials in your Seqera environment. 8. In the **Pipeline work directory** field, add the Azure blob container created previously, e.g., `az://towerrgstorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 9. Set the **Config mode** to **Manual**. diff --git a/platform-enterprise_versioned_docs/version-23.3/compute-envs/google-cloud-batch.md b/platform-enterprise_versioned_docs/version-23.3/compute-envs/google-cloud-batch.md index 202eb2848..f10e31392 100644 --- a/platform-enterprise_versioned_docs/version-23.3/compute-envs/google-cloud-batch.md +++ b/platform-enterprise_versioned_docs/version-23.3/compute-envs/google-cloud-batch.md @@ -136,7 +136,7 @@ After your Google Cloud resources have been created, create a new Seqera compute 8. In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the location selected in the previous step. :::note - When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 9. (_Optional_) Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. @@ -173,7 +173,7 @@ See [Launch pipelines](../launch/launchpad) to start running pipelines in your G [create-sa]: https://cloud.google.com/iam/docs/service-accounts-create#creating [get-json]: https://cloud.google.com/iam/docs/keys-list-get#get-key [location]: https://cloud.google.com/compute/docs/regions-zones#available -[wave-docs]: https://www.nextflow.io/docs/latest/wave.html +[wave-docs]: https://docs.seqera.io/nextflow/wave [platform-fusion-docs]: ../supported_software/fusion/overview [pre-post-run-scripts]: ../launch/advanced#pre-and-post-run-scripts [resource-labels]: ../resource-labels/overview diff --git a/platform-enterprise_versioned_docs/version-23.3/compute-envs/google-cloud-lifesciences.md b/platform-enterprise_versioned_docs/version-23.3/compute-envs/google-cloud-lifesciences.md index e5de50ec4..09b2e2d88 100644 --- a/platform-enterprise_versioned_docs/version-23.3/compute-envs/google-cloud-lifesciences.md +++ b/platform-enterprise_versioned_docs/version-23.3/compute-envs/google-cloud-lifesciences.md @@ -121,7 +121,7 @@ You can create multiple credentials in your Seqera workspace. See [Credentials]( 8. In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the region selected in the previous step. :::note - When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 9. You can enable **Preemptible** to use preemptible instances, which have significantly reduced cost compared to on-demand instances. diff --git a/platform-enterprise_versioned_docs/version-23.3/compute-envs/hpc.md b/platform-enterprise_versioned_docs/version-23.3/compute-envs/hpc.md index 31ae7d01d..9a293d155 100644 --- a/platform-enterprise_versioned_docs/version-23.3/compute-envs/hpc.md +++ b/platform-enterprise_versioned_docs/version-23.3/compute-envs/hpc.md @@ -19,7 +19,7 @@ To launch pipelines into an **HPC** cluster from Seqera, the following requireme - The cluster should allow outbound connections to the Seqera web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Seqera HPC compute environment @@ -33,8 +33,8 @@ To create a new **HPC** compute environment: 6. Enter the absolute path of the **Work directory** to be used on the cluster. 7. Enter the absolute path of the **Launch directory** to be used on the cluster. If omitted, it will be the same as the work directory. 8. Enter the **Login hostname**. This is usually the hostname or public IP address of the cluster's login node. -9. Enter the **Head queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will be submitted. -10. Enter the **Compute queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will submit tasks. +9. Enter the **Head queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will be submitted. +10. Enter the **Compute queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will submit tasks. 11. Expand **Staging options** to include optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. 12. Specify custom **Environment variables** for the head job and/or compute jobs. 13. Configure any advanced options needed: diff --git a/platform-enterprise_versioned_docs/version-23.3/compute-envs/overview.md b/platform-enterprise_versioned_docs/version-23.3/compute-envs/overview.md index 81a174b08..39202d2d1 100644 --- a/platform-enterprise_versioned_docs/version-23.3/compute-envs/overview.md +++ b/platform-enterprise_versioned_docs/version-23.3/compute-envs/overview.md @@ -47,8 +47,8 @@ Some important considerations: - Seqera only supports NVIDIA GPUs. Select instances with NVIDIA GPUs for your GPU-dependent processes. - The **Enable GPUs** setting causes Batch Forge to specify the most current [AWS-recommended GPU-optimized ECS AMI](https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ecs-optimized_AMI.html) as the EC2 fleet AMI when creating the compute environment. This setting can be overridden by **AMI ID** in the advanced options. - The **Enable GPUs** setting alone does not deploy GPU instances in your compute environment. You must still specify GPU-enabled instance types in the **Advanced options > Instance types** field. -- Your Nextflow script must include [accelerator directives](https://www.nextflow.io/docs/latest/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. -- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: +- Your Nextflow script must include [accelerator directives](https://docs.seqera.io/nextflow/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. +- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://docs.seqera.io/nextflow/process#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: ```groovy process { diff --git a/platform-enterprise_versioned_docs/version-23.3/credentials/aws_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.3/credentials/aws_registry_credentials.md index 5a6bed5e3..ee930c2ed 100644 --- a/platform-enterprise_versioned_docs/version-23.3/credentials/aws_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.3/credentials/aws_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [aws, ecr, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-23.3/credentials/azure_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.3/credentials/azure_registry_credentials.md index 47e0184b7..a35a15b43 100644 --- a/platform-enterprise_versioned_docs/version-23.3/credentials/azure_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.3/credentials/azure_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [azure, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-23.3/credentials/docker_hub_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.3/credentials/docker_hub_registry_credentials.md index 1c1e376d6..8ce8339a4 100644 --- a/platform-enterprise_versioned_docs/version-23.3/credentials/docker_hub_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.3/credentials/docker_hub_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [docker, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-23.3/credentials/gitea_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.3/credentials/gitea_registry_credentials.md index 68942d36e..83f4668ed 100644 --- a/platform-enterprise_versioned_docs/version-23.3/credentials/gitea_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.3/credentials/gitea_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [gitea, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). Gitea container registries support [authentication][gitea-auth] using a personal access token. Use your personal access token as your password when you create your Gitea container registry credentials in Seqera. diff --git a/platform-enterprise_versioned_docs/version-23.3/credentials/github_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.3/credentials/github_registry_credentials.md index e69de52aa..f24937d55 100644 --- a/platform-enterprise_versioned_docs/version-23.3/credentials/github_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.3/credentials/github_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [github, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). GitHub Packages only supports [authentication][github-pat] using a personal access token (classic). Use your personal access token as your password when you create your GitHub container registry credentials in Seqera. diff --git a/platform-enterprise_versioned_docs/version-23.3/credentials/gitlab_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.3/credentials/gitlab_registry_credentials.md index 8a969ffbe..0acee7cc9 100644 --- a/platform-enterprise_versioned_docs/version-23.3/credentials/gitlab_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.3/credentials/gitlab_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [gitlab, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). If your organization enabled two-factor authentication (2FA) for your GitLab organization or project, you must use your [personal access token][gitlab-pat] as your password when you create your [GitLab container registry credentials][gitlab-cr]. diff --git a/platform-enterprise_versioned_docs/version-23.3/credentials/google_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.3/credentials/google_registry_credentials.md index 931f276bf..f95d8a434 100644 --- a/platform-enterprise_versioned_docs/version-23.3/credentials/google_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.3/credentials/google_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [google, container, registry, artifact, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-23.3/credentials/overview.md b/platform-enterprise_versioned_docs/version-23.3/credentials/overview.md index 6c45a55ae..5016f4eb4 100644 --- a/platform-enterprise_versioned_docs/version-23.3/credentials/overview.md +++ b/platform-enterprise_versioned_docs/version-23.3/credentials/overview.md @@ -7,7 +7,7 @@ tags: [credentials] Configure **workspace credentials** in Seqera Platform to store the access keys and tokens for your [compute environments](../compute-envs/overview) and [Git hosting services](../git/overview). -From version 22.3, you can configure **container registry credentials** to be used by the [Wave container service](https://nextflow.io/docs/latest/wave.html) to authenticate to private and public container registries like Docker Hub, Google Artifact Registry, Quay, etc. +From version 22.3, you can configure **container registry credentials** to be used by the [Wave container service](https://docs.seqera.io/nextflow/wave) to authenticate to private and public container registries like Docker Hub, Google Artifact Registry, Quay, etc. See the **Container registry credentials** section for registry-specific instructions. diff --git a/platform-enterprise_versioned_docs/version-23.3/credentials/quay_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.3/credentials/quay_registry_credentials.md index 9a160b73d..93563fa32 100644 --- a/platform-enterprise_versioned_docs/version-23.3/credentials/quay_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.3/credentials/quay_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [quay, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-23.3/enterprise/configuration/wave.md b/platform-enterprise_versioned_docs/version-23.3/enterprise/configuration/wave.md index 50e810a27..1a8244f57 100644 --- a/platform-enterprise_versioned_docs/version-23.3/enterprise/configuration/wave.md +++ b/platform-enterprise_versioned_docs/version-23.3/enterprise/configuration/wave.md @@ -7,7 +7,7 @@ tags: [wave, containers, configuration] From version 22.4, Seqera Platform Enterprise supports the Seqera Wave containers service for on-prem installations. -To learn more about Wave, see [Wave containers](https://wave.seqera.io). To learn more about Wave and Nextflow integration, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +To learn more about Wave, see [Wave containers](https://wave.seqera.io). To learn more about Wave and Nextflow integration, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). ## Pair your Seqera instance with Wave @@ -35,4 +35,4 @@ When these conditions are met, the Wave feature is available on the Seqera compu After Wave is enabled, you can use private container repositories and the Fusion file system in your Nextflow pipelines. -Wave can also be enabled in the Nextflow pipeline config file. See the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html) for more information. +Wave can also be enabled in the Nextflow pipeline config file. See the [Nextflow documentation](https://docs.seqera.io/nextflow/wave) for more information. diff --git a/platform-enterprise_versioned_docs/version-23.3/faqs.md b/platform-enterprise_versioned_docs/version-23.3/faqs.md index 0309f2e69..79484b535 100644 --- a/platform-enterprise_versioned_docs/version-23.3/faqs.md +++ b/platform-enterprise_versioned_docs/version-23.3/faqs.md @@ -98,7 +98,7 @@ This error can occur if you execute a DSL 1-based Nextflow workflow using [Nextf The `sleep` commands in your Nextflow workflows may differ in behavior depending on where they are: - If used within an `errorStrategy` block, the Groovy sleep function will be used (which takes its value in milliseconds). -- If used within a process script block, that language's sleep binary/method will be used. **Example:** [this BASH script](https://www.nextflow.io/docs/latest/metrics.html?highlight=sleep) uses the BASH sleep binary, which takes its value in seconds. +- If used within a process script block, that language's sleep binary/method will be used. **Example:** [this BASH script](https://docs.seqera.io/nextflow/metrics.html?highlight=sleep) uses the BASH sleep binary, which takes its value in seconds. ## Containers @@ -338,7 +338,7 @@ You can force your Nextflow head job to use DSL2 syntax via any of the following **Invoke Nextflow CLI run arguments during Seqera launch** -From Nextflow v22.09.1-edge, you can specify [Nextflow CLI run arguments](https://www.nextflow.io/docs/latest/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable via [pre-run script](./launch/advanced#pre-and-post-run-scripts): +From Nextflow v22.09.1-edge, you can specify [Nextflow CLI run arguments](https://docs.seqera.io/nextflow/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable via [pre-run script](./launch/advanced#pre-and-post-run-scripts): ``` # Example: @@ -363,7 +363,7 @@ Currently, you can resolve this by creating blank `main.nf` and `nextflow.config **Use multiple Nextflow configuration files for different environments** -The main `nextflow.config` file will always be imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) in the main `nextflow.config`. +The main `nextflow.config` file will always be imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://docs.seqera.io/nextflow/config#config-profiles) in the main `nextflow.config`. Example: @@ -476,7 +476,7 @@ process.afterScript = 'sleep 60' **Jobs remain in RUNNING status when a pipeline run is canceled** -Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: +Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://docs.seqera.io/nextflow/process#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: ```bash @@ -523,7 +523,7 @@ The Groovy shell used by Nextflow to execute your workflow has a hard limit on s 1. Remove any unnecessary code or comments from the script. 2. Move long script bodies into a separate script file in the pipeline `/bin` directory. -3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://www.nextflow.io/docs/latest/dsl2.html#modules). +3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://docs.seqera.io/nextflow/dsl2#modules). ## Nextflow Launcher @@ -811,10 +811,10 @@ The default Azure Batch implementation in Seqera Platform uses a single pool for 1. Create two Batch pools in Azure: - One Dedicated - One [Low priority](https://learn.microsoft.com/en-us/azure/batch/batch-spot-vms#differences-between-spot-and-low-priority-vms). - - **Note**: Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://www.nextflow.io/docs/latest/azure.html#requirements-on-pre-existing-named-pools). + - **Note**: Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://docs.seqera.io/nextflow/azure#requirements-on-pre-existing-named-pools). 2. Create a manual [Azure Batch](./compute-envs/azure-batch#manual) compute environment in Seqera Platform. 3. In **Compute pool name** (step 10 in the guide linked above), specify your dedicated Batch pool. -4. Specify the Low priority pool using the `process.queue` [directive](https://www.nextflow.io/docs/latest/process.html#queue) in your `nextflow.config` file (either via the launch form, or your pipeline repository's `nextflow.config` file). +4. Specify the Low priority pool using the `process.queue` [directive](https://docs.seqera.io/nextflow/process#queue) in your `nextflow.config` file (either via the launch form, or your pipeline repository's `nextflow.config` file). ### AKS diff --git a/platform-enterprise_versioned_docs/version-23.3/getting-started/deployment-options.md b/platform-enterprise_versioned_docs/version-23.3/getting-started/deployment-options.md index d3e17de64..e17700219 100644 --- a/platform-enterprise_versioned_docs/version-23.3/getting-started/deployment-options.md +++ b/platform-enterprise_versioned_docs/version-23.3/getting-started/deployment-options.md @@ -96,5 +96,5 @@ Bearer token support requires Nextflow version 20.10.0 or later. Set with the `N You can now monitor your workflow runs in the Seqera interface. To configure and execute Nextflow pipelines in cloud environments, see [compute environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-enterprise_versioned_docs/version-23.3/launch/advanced.md b/platform-enterprise_versioned_docs/version-23.3/launch/advanced.md index ba8b5efc4..6a963589a 100644 --- a/platform-enterprise_versioned_docs/version-23.3/launch/advanced.md +++ b/platform-enterprise_versioned_docs/version-23.3/launch/advanced.md @@ -15,7 +15,7 @@ The **Nextflow config file** field allows you to add settings to the Nextflow co Nextflow parameters defined in this field override the same parameters in your `nextflow.config` file. ::: -This text should follow the same syntax as the [Nextflow configuration file](https://www.nextflow.io/docs/latest/config.html#config-syntax). +This text should follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax). For example, modify the **manifest** section to give the pipeline a name and description that will show up in the Seqera monitoring section: diff --git a/platform-enterprise_versioned_docs/version-23.3/launch/cache-resume.mdx b/platform-enterprise_versioned_docs/version-23.3/launch/cache-resume.mdx index 558b0d2ad..ef47bd4d2 100644 --- a/platform-enterprise_versioned_docs/version-23.3/launch/cache-resume.mdx +++ b/platform-enterprise_versioned_docs/version-23.3/launch/cache-resume.mdx @@ -8,13 +8,13 @@ tags: [cache, launch, resume, relaunch] import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; -Nextflow maintains a [cache](https://www.nextflow.io/docs/latest/cache-and-resume.html) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. +Nextflow maintains a [cache](https://docs.seqera.io/nextflow/cache-and-resume) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. ## Cache directory -Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. +Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. -To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://www.nextflow.io/docs/latest/process.html#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). +To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://docs.seqera.io/nextflow/process#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). @@ -108,7 +108,7 @@ Kubernetes compute environments do not use cloud cache by default. To specify a Google Cloud Storage 1. See [these instructions](../compute-envs/google-cloud-batch#iam) to set up IAM and create a JSON key file for the custom service account with permissions to your Google Cloud storage account. - 2. If you run the [gcloud CLI authentication flow](https://nextflow.io/docs/edge/google.html#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. + 2. If you run the [gcloud CLI authentication flow](https://docs.seqera.io/nextflow/google#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. 3. Add the following to the **Nextflow Config file** field when you [launch](../launch/launchpad#launch-form) your pipeline: ```groovy diff --git a/platform-enterprise_versioned_docs/version-23.3/launch/launchpad.md b/platform-enterprise_versioned_docs/version-23.3/launch/launchpad.md index 868bd87e5..248f3009a 100644 --- a/platform-enterprise_versioned_docs/version-23.3/launch/launchpad.md +++ b/platform-enterprise_versioned_docs/version-23.3/launch/launchpad.md @@ -53,7 +53,7 @@ For more information on relaunch and resume, see [Cache and resume](./cache-resu 4. Enter a repository URL for the **Pipeline to launch** (e.g., `https://github.com/nf-core/rnaseq.git`). :::note -Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://www.nextflow.io/docs/latest/sharing.html) in the Nextflow docs for more details. +Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://docs.seqera.io/nextflow/sharing) in the Nextflow docs for more details. ::: 5. Select a **Revision number** to use a specific version of the pipeline (optional). The Git default branch (e.g. main or master) or `manifest.defaultBranch` in the Nextflow configuration will be used by default. @@ -63,7 +63,7 @@ Nextflow pipelines are Git repositories that can reside on any public or private The credentials associated with the compute environment must have access to the work directory (e.g., an S3 bucket). ::: -7. Select any **Config profiles** you wish to use. See [Nextflow Config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) for more details. +7. Select any **Config profiles** you wish to use. See [Nextflow Config profiles](https://docs.seqera.io/nextflow/config#config-profiles) for more details. 8. Enter any **Pipeline parameters** in YAML or JSON format: ``` diff --git a/platform-enterprise_versioned_docs/version-23.3/monitoring/overview.md b/platform-enterprise_versioned_docs/version-23.3/monitoring/overview.md index 8a35cf2d3..0c04d617d 100644 --- a/platform-enterprise_versioned_docs/version-23.3/monitoring/overview.md +++ b/platform-enterprise_versioned_docs/version-23.3/monitoring/overview.md @@ -12,7 +12,7 @@ The **Runs** tab contains all previous runs in the workspace. Each new or resume - `submitted`: Pending execution - `running`: Running - `succeeded`: Completed successfully -- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://www.nextflow.io/docs/latest/process.html#errorstrategy) +- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://docs.seqera.io/nextflow/process#errorstrategy) - `cancelled`: Stopped manually during execution - `unknown`: Indeterminate status diff --git a/platform-enterprise_versioned_docs/version-23.3/platform-enterprise.md b/platform-enterprise_versioned_docs/version-23.3/platform-enterprise.md index a8183541c..9ef1602bf 100644 --- a/platform-enterprise_versioned_docs/version-23.3/platform-enterprise.md +++ b/platform-enterprise_versioned_docs/version-23.3/platform-enterprise.md @@ -28,4 +28,4 @@ Request a [**demo**](https://seqera.io/demo "Seqera Enterprise Demo") to explore Nextflow is both a programming workflow language and an execution runtime that supports a wide range of execution platforms, including popular traditional grid scheduling systems such as Slurm and IBM LSF, and cloud services such as AWS, Azure, and Google Cloud Batch. -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/) to learn more. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/) to learn more. diff --git a/platform-enterprise_versioned_docs/version-23.3/secrets/overview.md b/platform-enterprise_versioned_docs/version-23.3/secrets/overview.md index d237367e2..b54b6d4fd 100644 --- a/platform-enterprise_versioned_docs/version-23.3/secrets/overview.md +++ b/platform-enterprise_versioned_docs/version-23.3/secrets/overview.md @@ -27,12 +27,12 @@ Secrets defined by a user have higher priority and will override any secrets wit ## Use secrets in workflows -When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://www.nextflow.io/docs/edge/secrets.html#process-secrets) for more information. +When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://docs.seqera.io/nextflow/secrets) for more information. Secrets are automatically deleted from the secret manager when the pipeline completes, successfully or unsuccessfully. -:::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +:::note +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: ## AWS Secrets Manager integration diff --git a/platform-enterprise_versioned_docs/version-23.3/supported_software/dragen/overview.md b/platform-enterprise_versioned_docs/version-23.3/supported_software/dragen/overview.md index 8751f62c2..2f71291c5 100644 --- a/platform-enterprise_versioned_docs/version-23.3/supported_software/dragen/overview.md +++ b/platform-enterprise_versioned_docs/version-23.3/supported_software/dragen/overview.md @@ -57,7 +57,7 @@ See the [dragen.nf](https://github.com/seqeralabs/nf-dragen/blob/master/modules/ } ``` - See the [Nextflow label docs](https://www.nextflow.io/docs/latest/process.html?highlight=label#label) for more information. + See the [Nextflow label docs](https://docs.seqera.io/nextflow/process.html?highlight=label#label) for more information. 2. Define secrets in Seqera: diff --git a/platform-enterprise_versioned_docs/version-23.4/compute-envs/aws-batch.md b/platform-enterprise_versioned_docs/version-23.4/compute-envs/aws-batch.md index c294d469d..fd39fe421 100644 --- a/platform-enterprise_versioned_docs/version-23.4/compute-envs/aws-batch.md +++ b/platform-enterprise_versioned_docs/version-23.4/compute-envs/aws-batch.md @@ -112,10 +112,10 @@ Batch Forge automatically creates resources that you may be charged for in your 9. Enter your S3 bucket path in the **Pipeline work directory** field, e.g., `s3://seqera-bucket`. This bucket must be in the same region chosen in the previous step. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: -10. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +10. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 11. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. When using Fusion v2 without fast instance storage (see below), the following EBS settings are applied to optimize file system performance: @@ -288,7 +288,7 @@ Your Seqera compute environment uses resources that you may be charged for in yo 8. Enter an S3 bucket path for the **Pipeline work directory**, e.g., `s3://seqera-bucket`. This bucket must be in the same region chosen in the previous step. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 9. Set the **Config mode** to **Manual**. diff --git a/platform-enterprise_versioned_docs/version-23.4/compute-envs/azure-batch.md b/platform-enterprise_versioned_docs/version-23.4/compute-envs/azure-batch.md index f17cf71c2..e1a14e841 100644 --- a/platform-enterprise_versioned_docs/version-23.4/compute-envs/azure-batch.md +++ b/platform-enterprise_versioned_docs/version-23.4/compute-envs/azure-batch.md @@ -146,7 +146,7 @@ Create a Batch Forge Azure Batch compute environment: 8. In the **Pipeline work directory** field, enter the Azure blob container created previously, e.g., `az://towerrgstorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 9. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. @@ -156,7 +156,7 @@ Create a Batch Forge Azure Batch compute environment: 13. Enter the **VMs count**. If autoscaling is enabled (default), this is the maximum number of VMs you wish the pool to scale up to. If autoscaling is disabled, this is the fixed number of virtual machines in the pool. 14. Enable **Autoscale** to scale up and down automatically, based on the number of pipeline tasks. The number of VMs will vary from **0** to **VMs count**. 15. Enable **Dispose resources** for Seqera to automatically delete the Batch pool if the compute environment is deleted on the platform. -16. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://www.nextflow.io/docs/latest/wave.html) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. +16. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://docs.seqera.io/nextflow/wave) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. 17. Apply [**Resource labels**](../resource-labels/overview). This will populate the **Metadata** fields of the Azure Batch pool. 18. Expand **Staging options** to include optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. 19. Specify custom **Environment variables** for the **Head job** and/or **Compute jobs**. @@ -194,7 +194,7 @@ Your Seqera compute environment uses resources that you may be charged for in yo 8. In the **Pipeline work directory** field, add the Azure blob container created previously, e.g., `az://towerrgstorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 9. Set the **Config mode** to **Manual**. diff --git a/platform-enterprise_versioned_docs/version-23.4/compute-envs/google-cloud-batch.md b/platform-enterprise_versioned_docs/version-23.4/compute-envs/google-cloud-batch.md index b6487055b..297f3327d 100644 --- a/platform-enterprise_versioned_docs/version-23.4/compute-envs/google-cloud-batch.md +++ b/platform-enterprise_versioned_docs/version-23.4/compute-envs/google-cloud-batch.md @@ -147,7 +147,7 @@ Select the **Location** where you will execute your pipelines. See [Location][lo In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the location selected in the previous step. :::note -When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. +When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: #### Seqera features @@ -195,7 +195,7 @@ If you use VM instance templates for the head or compute jobs (see step 6 below) :::caution Seqera does not validate the VM instance template you specify in these fields. Generally, use templates that define only the machine type, network, disk, and configuration values that will not change across multiple VM instances and Seqera compute environments. See [Create instance templates](https://cloud.google.com/compute/docs/instance-templates/create-instance-templates) for instructions to create your instance templates. - To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://www.nextflow.io/docs/latest/google.html#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://www.nextflow.io/docs/latest/config.html#config-process-selectors) to assign separate templates to each of your processes. + To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://docs.seqera.io/nextflow/google#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://docs.seqera.io/nextflow/config#config-process-selectors) to assign separate templates to each of your processes. ::: Select **Create** to finalize the compute environment setup. @@ -206,7 +206,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [create-sa]: https://cloud.google.com/iam/docs/service-accounts-create#creating [get-json]: https://cloud.google.com/iam/docs/keys-list-get#get-key [location]: https://cloud.google.com/compute/docs/regions-zones#available -[wave-docs]: https://www.nextflow.io/docs/latest/wave.html +[wave-docs]: https://docs.seqera.io/nextflow/wave [platform-fusion-docs]: ../supported_software/fusion/overview [pre-post-run-scripts]: ../launch/advanced#pre-and-post-run-scripts [resource-labels]: ../resource-labels/overview diff --git a/platform-enterprise_versioned_docs/version-23.4/compute-envs/google-cloud-lifesciences.md b/platform-enterprise_versioned_docs/version-23.4/compute-envs/google-cloud-lifesciences.md index e5de50ec4..09b2e2d88 100644 --- a/platform-enterprise_versioned_docs/version-23.4/compute-envs/google-cloud-lifesciences.md +++ b/platform-enterprise_versioned_docs/version-23.4/compute-envs/google-cloud-lifesciences.md @@ -121,7 +121,7 @@ You can create multiple credentials in your Seqera workspace. See [Credentials]( 8. In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the region selected in the previous step. :::note - When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 9. You can enable **Preemptible** to use preemptible instances, which have significantly reduced cost compared to on-demand instances. diff --git a/platform-enterprise_versioned_docs/version-23.4/compute-envs/hpc.md b/platform-enterprise_versioned_docs/version-23.4/compute-envs/hpc.md index 31ae7d01d..9a293d155 100644 --- a/platform-enterprise_versioned_docs/version-23.4/compute-envs/hpc.md +++ b/platform-enterprise_versioned_docs/version-23.4/compute-envs/hpc.md @@ -19,7 +19,7 @@ To launch pipelines into an **HPC** cluster from Seqera, the following requireme - The cluster should allow outbound connections to the Seqera web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Seqera HPC compute environment @@ -33,8 +33,8 @@ To create a new **HPC** compute environment: 6. Enter the absolute path of the **Work directory** to be used on the cluster. 7. Enter the absolute path of the **Launch directory** to be used on the cluster. If omitted, it will be the same as the work directory. 8. Enter the **Login hostname**. This is usually the hostname or public IP address of the cluster's login node. -9. Enter the **Head queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will be submitted. -10. Enter the **Compute queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will submit tasks. +9. Enter the **Head queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will be submitted. +10. Enter the **Compute queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will submit tasks. 11. Expand **Staging options** to include optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. 12. Specify custom **Environment variables** for the head job and/or compute jobs. 13. Configure any advanced options needed: diff --git a/platform-enterprise_versioned_docs/version-23.4/compute-envs/overview.md b/platform-enterprise_versioned_docs/version-23.4/compute-envs/overview.md index 81a174b08..39202d2d1 100644 --- a/platform-enterprise_versioned_docs/version-23.4/compute-envs/overview.md +++ b/platform-enterprise_versioned_docs/version-23.4/compute-envs/overview.md @@ -47,8 +47,8 @@ Some important considerations: - Seqera only supports NVIDIA GPUs. Select instances with NVIDIA GPUs for your GPU-dependent processes. - The **Enable GPUs** setting causes Batch Forge to specify the most current [AWS-recommended GPU-optimized ECS AMI](https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ecs-optimized_AMI.html) as the EC2 fleet AMI when creating the compute environment. This setting can be overridden by **AMI ID** in the advanced options. - The **Enable GPUs** setting alone does not deploy GPU instances in your compute environment. You must still specify GPU-enabled instance types in the **Advanced options > Instance types** field. -- Your Nextflow script must include [accelerator directives](https://www.nextflow.io/docs/latest/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. -- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: +- Your Nextflow script must include [accelerator directives](https://docs.seqera.io/nextflow/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. +- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://docs.seqera.io/nextflow/process#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: ```groovy process { diff --git a/platform-enterprise_versioned_docs/version-23.4/credentials/aws_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.4/credentials/aws_registry_credentials.md index a5648e450..cfd50f81b 100644 --- a/platform-enterprise_versioned_docs/version-23.4/credentials/aws_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.4/credentials/aws_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [aws, ecr, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-23.4/credentials/azure_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.4/credentials/azure_registry_credentials.md index 47e0184b7..a35a15b43 100644 --- a/platform-enterprise_versioned_docs/version-23.4/credentials/azure_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.4/credentials/azure_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [azure, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-23.4/credentials/docker_hub_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.4/credentials/docker_hub_registry_credentials.md index 1c1e376d6..8ce8339a4 100644 --- a/platform-enterprise_versioned_docs/version-23.4/credentials/docker_hub_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.4/credentials/docker_hub_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [docker, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-23.4/credentials/gitea_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.4/credentials/gitea_registry_credentials.md index 68942d36e..83f4668ed 100644 --- a/platform-enterprise_versioned_docs/version-23.4/credentials/gitea_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.4/credentials/gitea_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [gitea, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). Gitea container registries support [authentication][gitea-auth] using a personal access token. Use your personal access token as your password when you create your Gitea container registry credentials in Seqera. diff --git a/platform-enterprise_versioned_docs/version-23.4/credentials/github_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.4/credentials/github_registry_credentials.md index e69de52aa..f24937d55 100644 --- a/platform-enterprise_versioned_docs/version-23.4/credentials/github_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.4/credentials/github_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [github, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). GitHub Packages only supports [authentication][github-pat] using a personal access token (classic). Use your personal access token as your password when you create your GitHub container registry credentials in Seqera. diff --git a/platform-enterprise_versioned_docs/version-23.4/credentials/gitlab_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.4/credentials/gitlab_registry_credentials.md index 8a969ffbe..0acee7cc9 100644 --- a/platform-enterprise_versioned_docs/version-23.4/credentials/gitlab_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.4/credentials/gitlab_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [gitlab, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). If your organization enabled two-factor authentication (2FA) for your GitLab organization or project, you must use your [personal access token][gitlab-pat] as your password when you create your [GitLab container registry credentials][gitlab-cr]. diff --git a/platform-enterprise_versioned_docs/version-23.4/credentials/google_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.4/credentials/google_registry_credentials.md index 931f276bf..f95d8a434 100644 --- a/platform-enterprise_versioned_docs/version-23.4/credentials/google_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.4/credentials/google_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [google, container, registry, artifact, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-23.4/credentials/overview.md b/platform-enterprise_versioned_docs/version-23.4/credentials/overview.md index 6c45a55ae..5016f4eb4 100644 --- a/platform-enterprise_versioned_docs/version-23.4/credentials/overview.md +++ b/platform-enterprise_versioned_docs/version-23.4/credentials/overview.md @@ -7,7 +7,7 @@ tags: [credentials] Configure **workspace credentials** in Seqera Platform to store the access keys and tokens for your [compute environments](../compute-envs/overview) and [Git hosting services](../git/overview). -From version 22.3, you can configure **container registry credentials** to be used by the [Wave container service](https://nextflow.io/docs/latest/wave.html) to authenticate to private and public container registries like Docker Hub, Google Artifact Registry, Quay, etc. +From version 22.3, you can configure **container registry credentials** to be used by the [Wave container service](https://docs.seqera.io/nextflow/wave) to authenticate to private and public container registries like Docker Hub, Google Artifact Registry, Quay, etc. See the **Container registry credentials** section for registry-specific instructions. diff --git a/platform-enterprise_versioned_docs/version-23.4/credentials/quay_registry_credentials.md b/platform-enterprise_versioned_docs/version-23.4/credentials/quay_registry_credentials.md index 9a160b73d..93563fa32 100644 --- a/platform-enterprise_versioned_docs/version-23.4/credentials/quay_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-23.4/credentials/quay_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [quay, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-23.4/enterprise/configuration/wave.md b/platform-enterprise_versioned_docs/version-23.4/enterprise/configuration/wave.md index 50e810a27..1a8244f57 100644 --- a/platform-enterprise_versioned_docs/version-23.4/enterprise/configuration/wave.md +++ b/platform-enterprise_versioned_docs/version-23.4/enterprise/configuration/wave.md @@ -7,7 +7,7 @@ tags: [wave, containers, configuration] From version 22.4, Seqera Platform Enterprise supports the Seqera Wave containers service for on-prem installations. -To learn more about Wave, see [Wave containers](https://wave.seqera.io). To learn more about Wave and Nextflow integration, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +To learn more about Wave, see [Wave containers](https://wave.seqera.io). To learn more about Wave and Nextflow integration, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). ## Pair your Seqera instance with Wave @@ -35,4 +35,4 @@ When these conditions are met, the Wave feature is available on the Seqera compu After Wave is enabled, you can use private container repositories and the Fusion file system in your Nextflow pipelines. -Wave can also be enabled in the Nextflow pipeline config file. See the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html) for more information. +Wave can also be enabled in the Nextflow pipeline config file. See the [Nextflow documentation](https://docs.seqera.io/nextflow/wave) for more information. diff --git a/platform-enterprise_versioned_docs/version-23.4/faqs.md b/platform-enterprise_versioned_docs/version-23.4/faqs.md index 860b775cb..6084a3acb 100644 --- a/platform-enterprise_versioned_docs/version-23.4/faqs.md +++ b/platform-enterprise_versioned_docs/version-23.4/faqs.md @@ -98,7 +98,7 @@ This error can occur if you execute a DSL 1-based Nextflow workflow using [Nextf The `sleep` commands in your Nextflow workflows may differ in behavior depending on where they are: - If used within an `errorStrategy` block, the Groovy sleep function will be used (which takes its value in milliseconds). -- If used within a process script block, that language's sleep binary/method will be used. **Example:** [this BASH script](https://www.nextflow.io/docs/latest/metrics.html?highlight=sleep) uses the BASH sleep binary, which takes its value in seconds. +- If used within a process script block, that language's sleep binary/method will be used. **Example:** [this BASH script](https://docs.seqera.io/nextflow/metrics.html?highlight=sleep) uses the BASH sleep binary, which takes its value in seconds. ## Containers @@ -338,7 +338,7 @@ You can force your Nextflow head job to use DSL2 syntax via any of the following **Invoke Nextflow CLI run arguments during Seqera launch** -From Nextflow v22.09.1-edge, you can specify [Nextflow CLI run arguments](https://www.nextflow.io/docs/latest/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable via [pre-run script](./launch/advanced#pre-and-post-run-scripts): +From Nextflow v22.09.1-edge, you can specify [Nextflow CLI run arguments](https://docs.seqera.io/nextflow/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable via [pre-run script](./launch/advanced#pre-and-post-run-scripts): ``` # Example: @@ -363,7 +363,7 @@ Currently, you can resolve this by creating blank `main.nf` and `nextflow.config **Use multiple Nextflow configuration files for different environments** -The main `nextflow.config` file will always be imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) in the main `nextflow.config`. +The main `nextflow.config` file will always be imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://docs.seqera.io/nextflow/config#config-profiles) in the main `nextflow.config`. Example: @@ -476,7 +476,7 @@ process.afterScript = 'sleep 60' **Jobs remain in RUNNING status when a pipeline run is canceled** -Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: +Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://docs.seqera.io/nextflow/process#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: ```bash @@ -523,7 +523,7 @@ The Groovy shell used by Nextflow to execute your workflow has a hard limit on s 1. Remove any unnecessary code or comments from the script. 2. Move long script bodies into a separate script file in the pipeline `/bin` directory. -3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://www.nextflow.io/docs/latest/dsl2.html#modules). +3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://docs.seqera.io/nextflow/dsl2#modules). ## Nextflow Launcher @@ -811,10 +811,10 @@ The default Azure Batch implementation in Seqera Platform uses a single pool for 1. Create two Batch pools in Azure: - One Dedicated - One [Low priority](https://learn.microsoft.com/en-us/azure/batch/batch-spot-vms#differences-between-spot-and-low-priority-vms). - - **Note**: Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://www.nextflow.io/docs/latest/azure.html#requirements-on-pre-existing-named-pools). + - **Note**: Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://docs.seqera.io/nextflow/azure#requirements-on-pre-existing-named-pools). 2. Create a manual [Azure Batch](./compute-envs/azure-batch#manual) compute environment in Seqera Platform. 3. In **Compute pool name** (step 10 in the guide linked above), specify your dedicated Batch pool. -4. Specify the Low priority pool using the `process.queue` [directive](https://www.nextflow.io/docs/latest/process.html#queue) in your `nextflow.config` file (either via the launch form, or your pipeline repository's `nextflow.config` file). +4. Specify the Low priority pool using the `process.queue` [directive](https://docs.seqera.io/nextflow/process#queue) in your `nextflow.config` file (either via the launch form, or your pipeline repository's `nextflow.config` file). ### AKS diff --git a/platform-enterprise_versioned_docs/version-23.4/getting-started/deployment-options.md b/platform-enterprise_versioned_docs/version-23.4/getting-started/deployment-options.md index 2bf291be4..2c6fb354f 100644 --- a/platform-enterprise_versioned_docs/version-23.4/getting-started/deployment-options.md +++ b/platform-enterprise_versioned_docs/version-23.4/getting-started/deployment-options.md @@ -96,5 +96,5 @@ Bearer token support requires Nextflow version 20.10.0 or later. Set with the `N You can now monitor your workflow runs in the Seqera interface. To configure and execute Nextflow pipelines in cloud environments, see [compute environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-enterprise_versioned_docs/version-23.4/getting-started/quickstart-demo/launch-pipelines.mdx b/platform-enterprise_versioned_docs/version-23.4/getting-started/quickstart-demo/launch-pipelines.mdx index e97fc8702..f530eb6a5 100644 --- a/platform-enterprise_versioned_docs/version-23.4/getting-started/quickstart-demo/launch-pipelines.mdx +++ b/platform-enterprise_versioned_docs/version-23.4/getting-started/quickstart-demo/launch-pipelines.mdx @@ -47,7 +47,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- (*Optional*) **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. +- (*Optional*) **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - (*Optional*) **Labels**: Assign new or existing [labels](../../labels/overview) to the run. - **Compute environment**: Select an existing workspace [compute environment](../../compute-envs/overview). diff --git a/platform-enterprise_versioned_docs/version-23.4/getting-started/rnaseq.mdx b/platform-enterprise_versioned_docs/version-23.4/getting-started/rnaseq.mdx index 9a16223c0..2aa8a486b 100644 --- a/platform-enterprise_versioned_docs/version-23.4/getting-started/rnaseq.mdx +++ b/platform-enterprise_versioned_docs/version-23.4/getting-started/rnaseq.mdx @@ -199,7 +199,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-enterprise_versioned_docs/version-23.4/launch/advanced.md b/platform-enterprise_versioned_docs/version-23.4/launch/advanced.md index 8922bfe7c..acf1c21e7 100644 --- a/platform-enterprise_versioned_docs/version-23.4/launch/advanced.md +++ b/platform-enterprise_versioned_docs/version-23.4/launch/advanced.md @@ -15,7 +15,7 @@ The **Nextflow config file** field allows you to add settings to the Nextflow co Nextflow parameters defined in this field override the same parameters in your `nextflow.config` file. ::: -This text should follow the same syntax as the [Nextflow configuration file](https://www.nextflow.io/docs/latest/config.html#config-syntax). +This text should follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax). For example, modify the **manifest** section to give the pipeline a name and description that will show up in the Seqera monitoring section: diff --git a/platform-enterprise_versioned_docs/version-23.4/launch/cache-resume.mdx b/platform-enterprise_versioned_docs/version-23.4/launch/cache-resume.mdx index 558b0d2ad..ef47bd4d2 100644 --- a/platform-enterprise_versioned_docs/version-23.4/launch/cache-resume.mdx +++ b/platform-enterprise_versioned_docs/version-23.4/launch/cache-resume.mdx @@ -8,13 +8,13 @@ tags: [cache, launch, resume, relaunch] import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; -Nextflow maintains a [cache](https://www.nextflow.io/docs/latest/cache-and-resume.html) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. +Nextflow maintains a [cache](https://docs.seqera.io/nextflow/cache-and-resume) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. ## Cache directory -Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. +Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. -To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://www.nextflow.io/docs/latest/process.html#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). +To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://docs.seqera.io/nextflow/process#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). @@ -108,7 +108,7 @@ Kubernetes compute environments do not use cloud cache by default. To specify a Google Cloud Storage 1. See [these instructions](../compute-envs/google-cloud-batch#iam) to set up IAM and create a JSON key file for the custom service account with permissions to your Google Cloud storage account. - 2. If you run the [gcloud CLI authentication flow](https://nextflow.io/docs/edge/google.html#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. + 2. If you run the [gcloud CLI authentication flow](https://docs.seqera.io/nextflow/google#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. 3. Add the following to the **Nextflow Config file** field when you [launch](../launch/launchpad#launch-form) your pipeline: ```groovy diff --git a/platform-enterprise_versioned_docs/version-23.4/launch/launchpad.md b/platform-enterprise_versioned_docs/version-23.4/launch/launchpad.md index 68a8aefca..2811319c6 100644 --- a/platform-enterprise_versioned_docs/version-23.4/launch/launchpad.md +++ b/platform-enterprise_versioned_docs/version-23.4/launch/launchpad.md @@ -52,14 +52,14 @@ For more information on relaunch and resume, see [Cache and resume](./cache-resu 1. Select a **Compute environment** from the available options. See [Compute environments](../compute-envs/overview) to learn how to create an environment for your preferred execution platform. 1. Enter a repository URL for the **Pipeline to launch** (e.g., `https://github.com/nf-core/rnaseq.git`). :::note - Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://www.nextflow.io/docs/latest/sharing.html) in the Nextflow docs for more details. + Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://docs.seqera.io/nextflow/sharing) in the Nextflow docs for more details. ::: 1. Select a **Revision number** to use a specific version of the pipeline (optional). The Git default branch (e.g. main or master) or `manifest.defaultBranch` in the Nextflow configuration will be used by default. 1. Enter the **Work directory**, which corresponds to the Nextflow work directory. You can also **Browse** for a cloud storage directory with Data Explorer. The default work directory of the compute environment will be used by default. :::note The credentials associated with the compute environment must have access to the work directory (e.g., an S3 bucket). ::: -1. Select any **Config profiles** you wish to use. See [Nextflow Config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) for more details. +1. Select any **Config profiles** you wish to use. See [Nextflow Config profiles](https://docs.seqera.io/nextflow/config#config-profiles) for more details. 1. Enter any **Pipeline parameters** in YAML or JSON format: ``` reads: 's3://nf-bucket/exome-data/ERR013140_{1,2}.fastq.bz2' @@ -72,7 +72,7 @@ For more information on relaunch and resume, see [Cache and resume](./cache-resu 1. Select or create [resource labels](../resource-labels/overview) to apply to the resources consumed by the run, if needed. 1. Expand the [Pipeline secrets](../secrets/overview) dropdown to select user or workspace secrets to be used during the run, if needed. :::note - In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). + In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: 1. Apply any [Advanced options](./advanced), if needed. 1. When you have filled the necessary launch form details, select **Launch**. The **Runs** tab shows your new run in a **submitted** status on the top of the list. Select the run name to navigate to the run detail page and view the configuration, parameters, status of individual tasks, and run report. diff --git a/platform-enterprise_versioned_docs/version-23.4/monitoring/overview.md b/platform-enterprise_versioned_docs/version-23.4/monitoring/overview.md index 8a35cf2d3..0c04d617d 100644 --- a/platform-enterprise_versioned_docs/version-23.4/monitoring/overview.md +++ b/platform-enterprise_versioned_docs/version-23.4/monitoring/overview.md @@ -12,7 +12,7 @@ The **Runs** tab contains all previous runs in the workspace. Each new or resume - `submitted`: Pending execution - `running`: Running - `succeeded`: Completed successfully -- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://www.nextflow.io/docs/latest/process.html#errorstrategy) +- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://docs.seqera.io/nextflow/process#errorstrategy) - `cancelled`: Stopped manually during execution - `unknown`: Indeterminate status diff --git a/platform-enterprise_versioned_docs/version-23.4/platform-enterprise.md b/platform-enterprise_versioned_docs/version-23.4/platform-enterprise.md index fe4b9c7cd..33a186eca 100644 --- a/platform-enterprise_versioned_docs/version-23.4/platform-enterprise.md +++ b/platform-enterprise_versioned_docs/version-23.4/platform-enterprise.md @@ -28,4 +28,4 @@ Request a [**demo**](https://seqera.io/demo "Seqera Enterprise Demo") to explore Nextflow is both a programming workflow language and an execution runtime that supports a wide range of execution platforms, including popular traditional grid scheduling systems such as Slurm and IBM LSF, and cloud services such as AWS, Azure, and Google Cloud Batch. -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/) to learn more. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/) to learn more. diff --git a/platform-enterprise_versioned_docs/version-23.4/reports/overview.md b/platform-enterprise_versioned_docs/version-23.4/reports/overview.md index ce92bd5a2..05c11a2be 100644 --- a/platform-enterprise_versioned_docs/version-23.4/reports/overview.md +++ b/platform-enterprise_versioned_docs/version-23.4/reports/overview.md @@ -76,10 +76,10 @@ By default, the MIME type is deduced from the file extension, so you don't need Nextflow can generate a number of built-in reports: -- [Execution report](https://nextflow.io/docs/latest/tracing.html#execution-report) -- [Execution timeline](https://nextflow.io/docs/latest/tracing.html#timeline-report) -- [Trace file](https://nextflow.io/docs/latest/tracing.html#trace-report) -- [Workflow diagram](https://nextflow.io/docs/latest/tracing.html#dag-visualisation) (i.e. DAG) +- [Execution report](https://docs.seqera.io/nextflow/tracing#execution-report) +- [Execution timeline](https://docs.seqera.io/nextflow/tracing#timeline-report) +- [Trace file](https://docs.seqera.io/nextflow/tracing#trace-report) +- [Workflow diagram](https://docs.seqera.io/nextflow/tracing#dag-visualisation) (i.e. DAG) In Nextflow version 24.03.0-edge and later, these reports can be included as pipeline reports in Seqera Platform. Specify them in `tower.yml` like any other file: diff --git a/platform-enterprise_versioned_docs/version-23.4/secrets/overview.md b/platform-enterprise_versioned_docs/version-23.4/secrets/overview.md index 7ba61f4ee..5d7c02330 100644 --- a/platform-enterprise_versioned_docs/version-23.4/secrets/overview.md +++ b/platform-enterprise_versioned_docs/version-23.4/secrets/overview.md @@ -31,12 +31,12 @@ Secrets defined by a user have higher priority and will override any secrets wit ## Use secrets in workflows -When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://www.nextflow.io/docs/edge/secrets.html#process-secrets) for more information. +When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://docs.seqera.io/nextflow/secrets) for more information. Secrets are automatically deleted from the secret manager when the pipeline completes, successfully or unsuccessfully. -:::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +:::note +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: ## AWS Secrets Manager integration diff --git a/platform-enterprise_versioned_docs/version-23.4/supported_software/dragen/overview.md b/platform-enterprise_versioned_docs/version-23.4/supported_software/dragen/overview.md index 221892aaa..4b0545fd6 100644 --- a/platform-enterprise_versioned_docs/version-23.4/supported_software/dragen/overview.md +++ b/platform-enterprise_versioned_docs/version-23.4/supported_software/dragen/overview.md @@ -57,7 +57,7 @@ See the [dragen.nf](https://github.com/seqeralabs/nf-dragen/blob/master/modules/ } ``` - See the [Nextflow label docs](https://www.nextflow.io/docs/latest/process.html?highlight=label#label) for more information. + See the [Nextflow label docs](https://docs.seqera.io/nextflow/process.html?highlight=label#label) for more information. 2. Define secrets in Seqera: diff --git a/platform-enterprise_versioned_docs/version-24.1/compute-envs/aws-batch.md b/platform-enterprise_versioned_docs/version-24.1/compute-envs/aws-batch.md index 45e8d9704..88f69367e 100644 --- a/platform-enterprise_versioned_docs/version-24.1/compute-envs/aws-batch.md +++ b/platform-enterprise_versioned_docs/version-24.1/compute-envs/aws-batch.md @@ -688,7 +688,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM 1. In the **Pipeline work directory** field type or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation), e.g., `s3://seqera-bucket`. The work directory can be customized to specify a folder inside the bucket where Nextflow intermediate files will be stored, e.g., `s3://seqera-bucket/nextflow-workdir`. The bucket must be located in the same region chosen in the previous step. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -697,7 +697,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM Using an EFS or FSx file system as your work directory is currently incompatible with [Data Studios](../data_studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Data Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
@@ -920,7 +920,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See 1. Select a **Region**, e.g., _eu-west-1 - Europe (Ireland)_. This region must match the region where your S3 bucket or EFS/FSx work directory is located to avoid high data transfer costs. 1. Enter or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation) in the **Pipeline work directory** field, e.g., `s3://seqera-bucket`. This bucket must be in the same region chosen in the previous step to avoid incurring high data transfer costs. The work directory can be customized to specify a folder inside the bucket, e.g., `s3://seqera-bucket/nextflow-workdir`. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -929,7 +929,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See Using an EFS or FSx file system as your work directory is currently incompatible with [Data Studios](../data_studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Data Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
diff --git a/platform-enterprise_versioned_docs/version-24.1/compute-envs/azure-batch.md b/platform-enterprise_versioned_docs/version-24.1/compute-envs/azure-batch.md index 716c20232..121d8b8fe 100644 --- a/platform-enterprise_versioned_docs/version-24.1/compute-envs/azure-batch.md +++ b/platform-enterprise_versioned_docs/version-24.1/compute-envs/azure-batch.md @@ -146,7 +146,7 @@ Create a Batch Forge compute environment: 1. In the **Pipeline work directory** field, enter the Azure blob container created previously, e.g., `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. @@ -156,7 +156,7 @@ Create a Batch Forge compute environment: 1. Enter the **VMs count**. If autoscaling is enabled (default), this is the maximum number of VMs you wish the pool to scale up to. If autoscaling is disabled, this is the fixed number of virtual machines in the pool. 1. Enable **Autoscale** to scale up and down automatically, based on the number of pipeline tasks. The number of VMs will vary from **0** to **VMs count**. 1. Enable **Dispose resources** for Seqera to automatically delete the Batch pool if the compute environment is deleted on the platform. -1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://www.nextflow.io/docs/latest/wave.html) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. +1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://docs.seqera.io/nextflow/wave) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. 1. Apply [**Resource labels**](../resource-labels/overview). This will populate the **Metadata** fields of the Batch pool. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. @@ -196,7 +196,7 @@ Your Seqera compute environment uses resources that you may be charged for in yo 1. Select a **Region**, e.g., _eastus (East US)_. 1. In the **Pipeline work directory** field, add the Azure blob container created previously, e.g., `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Set the **Config mode** to **Manual**. 1. Enter the **Compute Pool name**. This is the name of the Batch pool you created previously in the Azure Batch account. diff --git a/platform-enterprise_versioned_docs/version-24.1/compute-envs/google-cloud-batch.md b/platform-enterprise_versioned_docs/version-24.1/compute-envs/google-cloud-batch.md index 09dae5e4f..e542cc09f 100644 --- a/platform-enterprise_versioned_docs/version-24.1/compute-envs/google-cloud-batch.md +++ b/platform-enterprise_versioned_docs/version-24.1/compute-envs/google-cloud-batch.md @@ -147,7 +147,7 @@ Select the **Location** where you will execute your pipelines. See [Location][lo In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the location selected in the previous step. :::note -When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. +When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: #### Seqera features @@ -171,7 +171,7 @@ Select **Enable Fusion v2** to allow access to your Google Cloud Storage data vi :::note To specify virtual machine settings in Platform during compute environment creation, use the **Global Nextflow config** field to apply custom Nextflow process directives to all pipeline runs launched with this compute environment. - To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://www.nextflow.io/docs/latest/google.html#process-definition) for more information. + To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://docs.seqera.io/nextflow/google#process-definition) for more information. ::: When Fusion v2 is enabled, the following virtual machine settings are applied: @@ -227,7 +227,7 @@ If you use VM instance templates for the head or compute jobs (see step 6 below) :::caution Seqera does not validate the VM instance template you specify in these fields. Generally, use templates that define only the machine type, network, disk, and configuration values that will not change across multiple VM instances and Seqera compute environments. See [Create instance templates](https://cloud.google.com/compute/docs/instance-templates/create-instance-templates) for instructions to create your instance templates. - To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://www.nextflow.io/docs/latest/google.html#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://www.nextflow.io/docs/latest/config.html#config-process-selectors) to assign separate templates to each of your processes. + To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://docs.seqera.io/nextflow/google#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://docs.seqera.io/nextflow/config#config-process-selectors) to assign separate templates to each of your processes. ::: Select **Create** to finalize the compute environment setup. @@ -240,7 +240,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [create-sa]: https://cloud.google.com/iam/docs/service-accounts-create#creating [get-json]: https://cloud.google.com/iam/docs/keys-list-get#get-key [location]: https://cloud.google.com/compute/docs/regions-zones#available -[wave-docs]: https://www.nextflow.io/docs/latest/wave.html +[wave-docs]: https://docs.seqera.io/nextflow/wave [fusion-docs]: https://docs.seqera.io/fusion [platform-fusion-docs]: ../supported_software/fusion/overview [pre-post-run-scripts]: ../launch/advanced#pre-and-post-run-scripts diff --git a/platform-enterprise_versioned_docs/version-24.1/compute-envs/google-cloud-lifesciences.md b/platform-enterprise_versioned_docs/version-24.1/compute-envs/google-cloud-lifesciences.md index b4cb0c499..701ef68ae 100644 --- a/platform-enterprise_versioned_docs/version-24.1/compute-envs/google-cloud-lifesciences.md +++ b/platform-enterprise_versioned_docs/version-24.1/compute-envs/google-cloud-lifesciences.md @@ -121,7 +121,7 @@ You can create multiple credentials in your Seqera workspace. See [Credentials]( 8. In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the region selected in the previous step. :::note - When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 9. You can enable **Preemptible** to use preemptible instances, which have significantly reduced cost compared to on-demand instances. diff --git a/platform-enterprise_versioned_docs/version-24.1/compute-envs/hpc.md b/platform-enterprise_versioned_docs/version-24.1/compute-envs/hpc.md index ed65646d1..26d35eb3a 100644 --- a/platform-enterprise_versioned_docs/version-24.1/compute-envs/hpc.md +++ b/platform-enterprise_versioned_docs/version-24.1/compute-envs/hpc.md @@ -19,7 +19,7 @@ To launch pipelines into an **HPC** cluster from Seqera, the following requireme - The cluster should allow outbound connections to the Seqera web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Credentials @@ -64,8 +64,8 @@ To create a new **HPC** compute environment: 1. Enter the absolute path of the **Launch directory** to be used on the cluster. If omitted, it will be the same as the work directory. 1. Enter the **Login hostname**. This is usually the hostname or public IP address of the cluster's login node. -1. Enter the **Head queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will be submitted. -1. Enter the **Compute queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will submit tasks. +1. Enter the **Head queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will be submitted. +1. Enter the **Compute queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will submit tasks. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. diff --git a/platform-enterprise_versioned_docs/version-24.1/compute-envs/overview.md b/platform-enterprise_versioned_docs/version-24.1/compute-envs/overview.md index 81a174b08..39202d2d1 100644 --- a/platform-enterprise_versioned_docs/version-24.1/compute-envs/overview.md +++ b/platform-enterprise_versioned_docs/version-24.1/compute-envs/overview.md @@ -47,8 +47,8 @@ Some important considerations: - Seqera only supports NVIDIA GPUs. Select instances with NVIDIA GPUs for your GPU-dependent processes. - The **Enable GPUs** setting causes Batch Forge to specify the most current [AWS-recommended GPU-optimized ECS AMI](https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ecs-optimized_AMI.html) as the EC2 fleet AMI when creating the compute environment. This setting can be overridden by **AMI ID** in the advanced options. - The **Enable GPUs** setting alone does not deploy GPU instances in your compute environment. You must still specify GPU-enabled instance types in the **Advanced options > Instance types** field. -- Your Nextflow script must include [accelerator directives](https://www.nextflow.io/docs/latest/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. -- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: +- Your Nextflow script must include [accelerator directives](https://docs.seqera.io/nextflow/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. +- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://docs.seqera.io/nextflow/process#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: ```groovy process { diff --git a/platform-enterprise_versioned_docs/version-24.1/credentials/aws_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.1/credentials/aws_registry_credentials.md index a5648e450..cfd50f81b 100644 --- a/platform-enterprise_versioned_docs/version-24.1/credentials/aws_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.1/credentials/aws_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [aws, ecr, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-24.1/credentials/azure_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.1/credentials/azure_registry_credentials.md index 47e0184b7..a35a15b43 100644 --- a/platform-enterprise_versioned_docs/version-24.1/credentials/azure_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.1/credentials/azure_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [azure, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-24.1/credentials/docker_hub_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.1/credentials/docker_hub_registry_credentials.md index 1c1e376d6..8ce8339a4 100644 --- a/platform-enterprise_versioned_docs/version-24.1/credentials/docker_hub_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.1/credentials/docker_hub_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [docker, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-24.1/credentials/gitea_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.1/credentials/gitea_registry_credentials.md index 68942d36e..83f4668ed 100644 --- a/platform-enterprise_versioned_docs/version-24.1/credentials/gitea_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.1/credentials/gitea_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [gitea, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). Gitea container registries support [authentication][gitea-auth] using a personal access token. Use your personal access token as your password when you create your Gitea container registry credentials in Seqera. diff --git a/platform-enterprise_versioned_docs/version-24.1/credentials/github_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.1/credentials/github_registry_credentials.md index e69de52aa..f24937d55 100644 --- a/platform-enterprise_versioned_docs/version-24.1/credentials/github_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.1/credentials/github_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [github, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). GitHub Packages only supports [authentication][github-pat] using a personal access token (classic). Use your personal access token as your password when you create your GitHub container registry credentials in Seqera. diff --git a/platform-enterprise_versioned_docs/version-24.1/credentials/gitlab_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.1/credentials/gitlab_registry_credentials.md index 8a969ffbe..0acee7cc9 100644 --- a/platform-enterprise_versioned_docs/version-24.1/credentials/gitlab_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.1/credentials/gitlab_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [gitlab, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). If your organization enabled two-factor authentication (2FA) for your GitLab organization or project, you must use your [personal access token][gitlab-pat] as your password when you create your [GitLab container registry credentials][gitlab-cr]. diff --git a/platform-enterprise_versioned_docs/version-24.1/credentials/google_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.1/credentials/google_registry_credentials.md index 931f276bf..f95d8a434 100644 --- a/platform-enterprise_versioned_docs/version-24.1/credentials/google_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.1/credentials/google_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [google, container, registry, artifact, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-24.1/credentials/overview.md b/platform-enterprise_versioned_docs/version-24.1/credentials/overview.md index 6c45a55ae..5016f4eb4 100644 --- a/platform-enterprise_versioned_docs/version-24.1/credentials/overview.md +++ b/platform-enterprise_versioned_docs/version-24.1/credentials/overview.md @@ -7,7 +7,7 @@ tags: [credentials] Configure **workspace credentials** in Seqera Platform to store the access keys and tokens for your [compute environments](../compute-envs/overview) and [Git hosting services](../git/overview). -From version 22.3, you can configure **container registry credentials** to be used by the [Wave container service](https://nextflow.io/docs/latest/wave.html) to authenticate to private and public container registries like Docker Hub, Google Artifact Registry, Quay, etc. +From version 22.3, you can configure **container registry credentials** to be used by the [Wave container service](https://docs.seqera.io/nextflow/wave) to authenticate to private and public container registries like Docker Hub, Google Artifact Registry, Quay, etc. See the **Container registry credentials** section for registry-specific instructions. diff --git a/platform-enterprise_versioned_docs/version-24.1/credentials/quay_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.1/credentials/quay_registry_credentials.md index 9a160b73d..93563fa32 100644 --- a/platform-enterprise_versioned_docs/version-24.1/credentials/quay_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.1/credentials/quay_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [quay, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-24.1/enterprise/configuration/wave.md b/platform-enterprise_versioned_docs/version-24.1/enterprise/configuration/wave.md index 50e810a27..1a8244f57 100644 --- a/platform-enterprise_versioned_docs/version-24.1/enterprise/configuration/wave.md +++ b/platform-enterprise_versioned_docs/version-24.1/enterprise/configuration/wave.md @@ -7,7 +7,7 @@ tags: [wave, containers, configuration] From version 22.4, Seqera Platform Enterprise supports the Seqera Wave containers service for on-prem installations. -To learn more about Wave, see [Wave containers](https://wave.seqera.io). To learn more about Wave and Nextflow integration, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +To learn more about Wave, see [Wave containers](https://wave.seqera.io). To learn more about Wave and Nextflow integration, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). ## Pair your Seqera instance with Wave @@ -35,4 +35,4 @@ When these conditions are met, the Wave feature is available on the Seqera compu After Wave is enabled, you can use private container repositories and the Fusion file system in your Nextflow pipelines. -Wave can also be enabled in the Nextflow pipeline config file. See the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html) for more information. +Wave can also be enabled in the Nextflow pipeline config file. See the [Nextflow documentation](https://docs.seqera.io/nextflow/wave) for more information. diff --git a/platform-enterprise_versioned_docs/version-24.1/getting-started/deployment-options.md b/platform-enterprise_versioned_docs/version-24.1/getting-started/deployment-options.md index 304ffb33b..c0568990d 100644 --- a/platform-enterprise_versioned_docs/version-24.1/getting-started/deployment-options.md +++ b/platform-enterprise_versioned_docs/version-24.1/getting-started/deployment-options.md @@ -96,5 +96,5 @@ If you have an existing environment where you run Nextflow directly, you can sti You can now monitor your workflow runs in the Seqera interface. To configure and execute Nextflow pipelines in cloud environments, see [compute environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-enterprise_versioned_docs/version-24.1/getting-started/proteinfold.mdx b/platform-enterprise_versioned_docs/version-24.1/getting-started/proteinfold.mdx index cff163053..645459a90 100644 --- a/platform-enterprise_versioned_docs/version-24.1/getting-started/proteinfold.mdx +++ b/platform-enterprise_versioned_docs/version-24.1/getting-started/proteinfold.mdx @@ -186,7 +186,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL: `https://github.com/nf-core/proteinfold`. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name: `1.1.1`. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-enterprise_versioned_docs/version-24.1/getting-started/quickstart-demo/launch-pipelines.md b/platform-enterprise_versioned_docs/version-24.1/getting-started/quickstart-demo/launch-pipelines.md index 5fd38fb37..ae748622e 100644 --- a/platform-enterprise_versioned_docs/version-24.1/getting-started/quickstart-demo/launch-pipelines.md +++ b/platform-enterprise_versioned_docs/version-24.1/getting-started/quickstart-demo/launch-pipelines.md @@ -44,7 +44,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- (*Optional*) **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. +- (*Optional*) **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - (*Optional*) **Labels**: Assign new or existing [labels](../../labels/overview) to the run. - **Compute environment**: Select an existing workspace [compute environment](../../compute-envs/overview). diff --git a/platform-enterprise_versioned_docs/version-24.1/getting-started/rnaseq.mdx b/platform-enterprise_versioned_docs/version-24.1/getting-started/rnaseq.mdx index 7ad7677fc..ba13432a5 100644 --- a/platform-enterprise_versioned_docs/version-24.1/getting-started/rnaseq.mdx +++ b/platform-enterprise_versioned_docs/version-24.1/getting-started/rnaseq.mdx @@ -198,7 +198,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-enterprise_versioned_docs/version-24.1/launch/advanced.md b/platform-enterprise_versioned_docs/version-24.1/launch/advanced.md index 418a4751e..dd546c7b2 100644 --- a/platform-enterprise_versioned_docs/version-24.1/launch/advanced.md +++ b/platform-enterprise_versioned_docs/version-24.1/launch/advanced.md @@ -9,7 +9,7 @@ You can modify the configuration and execution of a pipeline with advanced launc ### Nextflow config file -Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://www.nextflow.io/docs/latest/config.html#config-syntax). +Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax). For example, modify the **manifest** section to give the pipeline a name and description that will show up in the Seqera monitoring section: @@ -106,7 +106,7 @@ Instruct Nextflow to pull the latest pipeline version from the Git repository. T ### Stub run -Replace Nextflow process commands with command [stubs](https://www.nextflow.io/docs/latest/process.html#stub), where defined, before execution. +Replace Nextflow process commands with command [stubs](https://docs.seqera.io/nextflow/process#stub), where defined, before execution. ### Main script diff --git a/platform-enterprise_versioned_docs/version-24.1/launch/cache-resume.mdx b/platform-enterprise_versioned_docs/version-24.1/launch/cache-resume.mdx index 558b0d2ad..ef47bd4d2 100644 --- a/platform-enterprise_versioned_docs/version-24.1/launch/cache-resume.mdx +++ b/platform-enterprise_versioned_docs/version-24.1/launch/cache-resume.mdx @@ -8,13 +8,13 @@ tags: [cache, launch, resume, relaunch] import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; -Nextflow maintains a [cache](https://www.nextflow.io/docs/latest/cache-and-resume.html) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. +Nextflow maintains a [cache](https://docs.seqera.io/nextflow/cache-and-resume) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. ## Cache directory -Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. +Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. -To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://www.nextflow.io/docs/latest/process.html#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). +To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://docs.seqera.io/nextflow/process#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). @@ -108,7 +108,7 @@ Kubernetes compute environments do not use cloud cache by default. To specify a Google Cloud Storage 1. See [these instructions](../compute-envs/google-cloud-batch#iam) to set up IAM and create a JSON key file for the custom service account with permissions to your Google Cloud storage account. - 2. If you run the [gcloud CLI authentication flow](https://nextflow.io/docs/edge/google.html#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. + 2. If you run the [gcloud CLI authentication flow](https://docs.seqera.io/nextflow/google#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. 3. Add the following to the **Nextflow Config file** field when you [launch](../launch/launchpad#launch-form) your pipeline: ```groovy diff --git a/platform-enterprise_versioned_docs/version-24.1/launch/launchpad.md b/platform-enterprise_versioned_docs/version-24.1/launch/launchpad.md index e4fafa6e5..0539f7db4 100644 --- a/platform-enterprise_versioned_docs/version-24.1/launch/launchpad.md +++ b/platform-enterprise_versioned_docs/version-24.1/launch/launchpad.md @@ -33,10 +33,10 @@ For saved pipelines, **General config** and **Run parameters** fields are prefil - **Pipeline to launch**: A Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. Private repositories require [access credentials](../credentials/overview). :::note - Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://www.nextflow.io/docs/latest/sharing.html) in the Nextflow docs for more details. + Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://docs.seqera.io/nextflow/sharing) in the Nextflow docs for more details. ::: - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: A unique identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: The [compute environment](../compute-envs/overview) where the run will be launched. @@ -76,7 +76,7 @@ Use resource labels to tag the computing resources created during the workflow e Secrets are used to store keys and tokens used by workflow tasks to interact with external systems. Enter the names of any stored user or workspace secrets required for the workflow execution. :::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: #### Advanced options diff --git a/platform-enterprise_versioned_docs/version-24.1/monitoring/overview.md b/platform-enterprise_versioned_docs/version-24.1/monitoring/overview.md index 8a35cf2d3..0c04d617d 100644 --- a/platform-enterprise_versioned_docs/version-24.1/monitoring/overview.md +++ b/platform-enterprise_versioned_docs/version-24.1/monitoring/overview.md @@ -12,7 +12,7 @@ The **Runs** tab contains all previous runs in the workspace. Each new or resume - `submitted`: Pending execution - `running`: Running - `succeeded`: Completed successfully -- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://www.nextflow.io/docs/latest/process.html#errorstrategy) +- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://docs.seqera.io/nextflow/process#errorstrategy) - `cancelled`: Stopped manually during execution - `unknown`: Indeterminate status diff --git a/platform-enterprise_versioned_docs/version-24.1/platform-enterprise.md b/platform-enterprise_versioned_docs/version-24.1/platform-enterprise.md index fe4b9c7cd..33a186eca 100644 --- a/platform-enterprise_versioned_docs/version-24.1/platform-enterprise.md +++ b/platform-enterprise_versioned_docs/version-24.1/platform-enterprise.md @@ -28,4 +28,4 @@ Request a [**demo**](https://seqera.io/demo "Seqera Enterprise Demo") to explore Nextflow is both a programming workflow language and an execution runtime that supports a wide range of execution platforms, including popular traditional grid scheduling systems such as Slurm and IBM LSF, and cloud services such as AWS, Azure, and Google Cloud Batch. -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/) to learn more. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/) to learn more. diff --git a/platform-enterprise_versioned_docs/version-24.1/reports/overview.md b/platform-enterprise_versioned_docs/version-24.1/reports/overview.md index c4ba99b1c..59db26855 100644 --- a/platform-enterprise_versioned_docs/version-24.1/reports/overview.md +++ b/platform-enterprise_versioned_docs/version-24.1/reports/overview.md @@ -82,10 +82,10 @@ By default, the MIME type is deduced from the file extension, so you don't need Nextflow can generate a number of built-in reports: -- [Execution report](https://nextflow.io/docs/latest/tracing.html#execution-report) -- [Execution timeline](https://nextflow.io/docs/latest/tracing.html#timeline-report) -- [Trace file](https://nextflow.io/docs/latest/tracing.html#trace-report) -- [Workflow diagram](https://nextflow.io/docs/latest/tracing.html#dag-visualisation) (i.e. DAG) +- [Execution report](https://docs.seqera.io/nextflow/tracing#execution-report) +- [Execution timeline](https://docs.seqera.io/nextflow/tracing#timeline-report) +- [Trace file](https://docs.seqera.io/nextflow/tracing#trace-report) +- [Workflow diagram](https://docs.seqera.io/nextflow/tracing#dag-visualisation) (i.e. DAG) In Nextflow version 24.03.0-edge and later, these reports can be included as pipeline reports in Seqera Platform. Specify them in `tower.yml` like any other file: diff --git a/platform-enterprise_versioned_docs/version-24.1/secrets/overview.md b/platform-enterprise_versioned_docs/version-24.1/secrets/overview.md index 7ba61f4ee..5d7c02330 100644 --- a/platform-enterprise_versioned_docs/version-24.1/secrets/overview.md +++ b/platform-enterprise_versioned_docs/version-24.1/secrets/overview.md @@ -31,12 +31,12 @@ Secrets defined by a user have higher priority and will override any secrets wit ## Use secrets in workflows -When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://www.nextflow.io/docs/edge/secrets.html#process-secrets) for more information. +When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://docs.seqera.io/nextflow/secrets) for more information. Secrets are automatically deleted from the secret manager when the pipeline completes, successfully or unsuccessfully. -:::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +:::note +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: ## AWS Secrets Manager integration diff --git a/platform-enterprise_versioned_docs/version-24.1/supported_software/dragen/overview.md b/platform-enterprise_versioned_docs/version-24.1/supported_software/dragen/overview.md index 7eaf0d4d4..1bbdb4833 100644 --- a/platform-enterprise_versioned_docs/version-24.1/supported_software/dragen/overview.md +++ b/platform-enterprise_versioned_docs/version-24.1/supported_software/dragen/overview.md @@ -57,7 +57,7 @@ See the [dragen.nf](https://github.com/seqeralabs/nf-dragen/blob/master/modules/ } ``` - See the [Nextflow label docs](https://www.nextflow.io/docs/latest/process.html?highlight=label#label) for more information. + See the [Nextflow label docs](https://docs.seqera.io/nextflow/process.html?highlight=label#label) for more information. 2. Define secrets in Seqera: diff --git a/platform-enterprise_versioned_docs/version-24.1/troubleshooting_and_faqs/azure_troubleshooting.md b/platform-enterprise_versioned_docs/version-24.1/troubleshooting_and_faqs/azure_troubleshooting.md index 9ce13e2e8..3c2430d43 100644 --- a/platform-enterprise_versioned_docs/version-24.1/troubleshooting_and_faqs/azure_troubleshooting.md +++ b/platform-enterprise_versioned_docs/version-24.1/troubleshooting_and_faqs/azure_troubleshooting.md @@ -20,12 +20,12 @@ The default Azure Batch implementation in Seqera Platform uses a single pool for - One [Low priority](https://learn.microsoft.com/en-us/azure/batch/batch-spot-vms#differences-between-spot-and-low-priority-vms) :::note -Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://www.nextflow.io/docs/latest/azure.html#requirements-on-pre-existing-named-pools). +Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://docs.seqera.io/nextflow/azure#requirements-on-pre-existing-named-pools). ::: 2. Create a manual [Azure Batch](../compute-envs/azure-batch#manual) compute environment in Seqera Platform. 3. In **Compute pool name**, specify your dedicated Batch pool. -4. Specify the Low priority pool using the `process.queue` [directive](https://www.nextflow.io/docs/latest/process.html#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. +4. Specify the Low priority pool using the `process.queue` [directive](https://docs.seqera.io/nextflow/process#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. ### Azure Kubernetes Service (AKS) diff --git a/platform-enterprise_versioned_docs/version-24.1/troubleshooting_and_faqs/nextflow.md b/platform-enterprise_versioned_docs/version-24.1/troubleshooting_and_faqs/nextflow.md index 27fad8801..a843d3b74 100644 --- a/platform-enterprise_versioned_docs/version-24.1/troubleshooting_and_faqs/nextflow.md +++ b/platform-enterprise_versioned_docs/version-24.1/troubleshooting_and_faqs/nextflow.md @@ -19,7 +19,7 @@ To minimize disruption on existing pipelines, version 22.1.x and later are confi **Invoke Nextflow CLI run arguments during Seqera launch** -From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://www.nextflow.io/docs/latest/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): +From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://docs.seqera.io/nextflow/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): ``` export NXF_CLI_OPTS='-dump-hashes' @@ -43,7 +43,7 @@ Currently, you can resolve this by creating empty `main.nf` and `nextflow.config **Use multiple Nextflow configuration files for different environments** -The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) in the main `nextflow.config`. +The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://docs.seqera.io/nextflow/config#config-profiles) in the main `nextflow.config`. Example: @@ -151,7 +151,7 @@ process.afterScript = 'sleep 60' **Jobs remain in RUNNING status when a pipeline run is canceled** -Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: +Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://docs.seqera.io/nextflow/process#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: ``` process terminateError { @@ -195,7 +195,7 @@ The Groovy shell used by Nextflow to execute your workflow has a hard limit on s 1. Remove any unnecessary code or comments from the script. 2. Move long script bodies into a separate script file in the pipeline `/bin` directory. -3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://www.nextflow.io/docs/latest/dsl2.html#modules). +3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://docs.seqera.io/nextflow/dsl2#modules). ### Nextflow Launcher diff --git a/platform-enterprise_versioned_docs/version-24.1/troubleshooting_and_faqs/troubleshooting.md b/platform-enterprise_versioned_docs/version-24.1/troubleshooting_and_faqs/troubleshooting.md index e2b833ce2..b831111dc 100644 --- a/platform-enterprise_versioned_docs/version-24.1/troubleshooting_and_faqs/troubleshooting.md +++ b/platform-enterprise_versioned_docs/version-24.1/troubleshooting_and_faqs/troubleshooting.md @@ -43,7 +43,7 @@ This error can occur if you execute a DSL1-based Nextflow workflow using [Nextfl The `sleep` commands in your Nextflow workflows may differ in behavior depending on where they are: - If used within an `errorStrategy` block, the Groovy sleep function will be used (which takes its value in milliseconds). -- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://www.nextflow.io/docs/latest/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. +- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://docs.seqera.io/nextflow/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. **Large number of batch job definitions** diff --git a/platform-enterprise_versioned_docs/version-24.2/compute-envs/aws-batch.md b/platform-enterprise_versioned_docs/version-24.2/compute-envs/aws-batch.md index aeb63d7a3..49ebe25f8 100644 --- a/platform-enterprise_versioned_docs/version-24.2/compute-envs/aws-batch.md +++ b/platform-enterprise_versioned_docs/version-24.2/compute-envs/aws-batch.md @@ -688,7 +688,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM 1. In the **Pipeline work directory** field type or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation), e.g., `s3://seqera-bucket`. The work directory can be customized to specify a folder inside the bucket where Nextflow intermediate files will be stored, e.g., `s3://seqera-bucket/nextflow-workdir`. The bucket must be located in the same region chosen in the previous step. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -697,7 +697,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM Using an EFS or FSx file system as your work directory is currently incompatible with [Data Studios](../data_studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Data Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
@@ -920,7 +920,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See 1. Select a **Region**, e.g., _eu-west-1 - Europe (Ireland)_. This region must match the region where your S3 bucket or EFS/FSx work directory is located to avoid high data transfer costs. 1. Enter or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation) in the **Pipeline work directory** field, e.g., `s3://seqera-bucket`. This bucket must be in the same region chosen in the previous step to avoid incurring high data transfer costs. The work directory can be customized to specify a folder inside the bucket, e.g., `s3://seqera-bucket/nextflow-workdir`. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -929,7 +929,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See Using an EFS or FSx file system as your work directory is currently incompatible with [Data Studios](../data_studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Data Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
diff --git a/platform-enterprise_versioned_docs/version-24.2/compute-envs/azure-batch.md b/platform-enterprise_versioned_docs/version-24.2/compute-envs/azure-batch.md index b2b52c74a..2dbe0ae6a 100644 --- a/platform-enterprise_versioned_docs/version-24.2/compute-envs/azure-batch.md +++ b/platform-enterprise_versioned_docs/version-24.2/compute-envs/azure-batch.md @@ -189,7 +189,7 @@ Nextflow can authenticate to Azure services using a managed identity. This metho When you use a manually-configured compute environment with a managed identity attached to the Azure Batch Pool, Nextflow can use this managed identity for authentication. However, Seqera still needs to use access keys or an Entra service principal to submit the initial task to Azure Batch to run Nextflow, which will then proceed with the managed identity for subsequent authentication. 1. In Azure, create a user-assigned managed identity. See [Manage user-assigned managed identities](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-manage-user-assigned-managed-identities) for detailed steps. Take note of the client ID of the managed identity when you create it. -1. The user-assigned managed identity must have the necessary access roles for Nextflow. See [Required role assignments](https://www.nextflow.io/docs/latest/azure.html#required-role-assignments) for more information. +1. The user-assigned managed identity must have the necessary access roles for Nextflow. See [Required role assignments](https://docs.seqera.io/nextflow/azure#required-role-assignments) for more information. 1. Associate the user-assigned managed identity with the Azure Batch Pool. See [Set up managed identity in your Batch pool](https://learn.microsoft.com/en-us/troubleshoot/azure/hpc/batch/use-managed-identities-azure-batch-account-pool#set-up-managed-identity-in-your-batch-pool) for more information. 1. When you set up the Seqera compute environment, select the Azure Batch pool by name and enter the managed identity client ID in the specified field as instructed above. @@ -252,7 +252,7 @@ Create a Batch Forge Azure Batch compute environment: 1. Select a **Region**, such as _eastus_. 1. In the **Pipeline work directory** field, enter the Azure blob container created previously. For example, `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. 1. Select **Enable Fusion v2** to allow access to your Azure Blob Storage data via the [Fusion v2][fusion-docs] virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. @@ -285,7 +285,7 @@ Create a Batch Forge Azure Batch compute environment: 1. Enter the **VMs count**. If autoscaling is enabled (default), this is the maximum number of VMs you wish the pool to scale up to. If autoscaling is disabled, this is the fixed number of virtual machines in the pool. 1. Enable **Autoscale** to scale up and down automatically, based on the number of pipeline tasks. The number of VMs will vary from **0** to **VMs count**. 1. Enable **Dispose resources** for Seqera to automatically delete the Batch pool if the compute environment is deleted on the platform. -1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://www.nextflow.io/docs/latest/wave.html) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. +1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://docs.seqera.io/nextflow/wave) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. 1. Apply [**Resource labels**](../resource-labels/overview). This will populate the **Metadata** fields of the Azure Batch pool. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. @@ -396,7 +396,7 @@ The following settings can be modified after creating a pool: 1. Select a **Region**, such as _eastus (East US)_. 1. In the **Pipeline work directory** field, add the Azure blob container created previously. For example, `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. 1. Select **Enable Fusion v2** to allow access to your Azure Blob Storage data via the [Fusion v2][fusion-docs] virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. @@ -463,7 +463,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [az-vm-gen]: https://learn.microsoft.com/en-us/azure/virtual-machines/generation-2 [az-disk-type]: https://learn.microsoft.com/en-us/azure/virtual-machines/disks-types [az-batch-autoscale]: https://learn.microsoft.com/en-us/azure/batch/batch-automatic-scaling -[az-file-shares]: https://www.nextflow.io/docs/latest/azure.html#azure-file-shares +[az-file-shares]: https://docs.seqera.io/nextflow/azure#azure-file-shares [az-vm-sizes]: https://learn.microsoft.com/en-us/azure/virtual-machines/sizes/overview [wave-docs]: https://docs.seqera.io/wave diff --git a/platform-enterprise_versioned_docs/version-24.2/compute-envs/google-cloud-batch.md b/platform-enterprise_versioned_docs/version-24.2/compute-envs/google-cloud-batch.md index 2474276b8..fb67fae47 100644 --- a/platform-enterprise_versioned_docs/version-24.2/compute-envs/google-cloud-batch.md +++ b/platform-enterprise_versioned_docs/version-24.2/compute-envs/google-cloud-batch.md @@ -147,7 +147,7 @@ Select the **Location** where you will execute your pipelines. See [Location][lo In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the location selected in the previous step. :::note -When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. +When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: #### Seqera features @@ -171,7 +171,7 @@ Select **Enable Fusion v2** to allow access to your Google Cloud Storage data vi :::note To specify virtual machine settings in Platform during compute environment creation, use the **Global Nextflow config** field to apply custom Nextflow process directives to all pipeline runs launched with this compute environment. - To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://www.nextflow.io/docs/latest/google.html#process-definition) for more information. + To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://docs.seqera.io/nextflow/google#process-definition) for more information. ::: When Fusion v2 is enabled, the following virtual machine settings are applied: @@ -231,7 +231,7 @@ If you use VM instance templates for the head or compute jobs (see step 6 below) :::caution Seqera does not validate the VM instance template you specify in these fields. Generally, use templates that define only the machine type, network, disk, and configuration values that will not change across multiple VM instances and Seqera compute environments. See [Create instance templates](https://cloud.google.com/compute/docs/instance-templates/create-instance-templates) for instructions to create your instance templates. - To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://www.nextflow.io/docs/latest/google.html#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://www.nextflow.io/docs/latest/config.html#config-process-selectors) to assign separate templates to each of your processes. + To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://docs.seqera.io/nextflow/google#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://docs.seqera.io/nextflow/config#config-process-selectors) to assign separate templates to each of your processes. ::: Select **Create** to finalize the compute environment setup. @@ -244,7 +244,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [create-sa]: https://cloud.google.com/iam/docs/service-accounts-create#creating [get-json]: https://cloud.google.com/iam/docs/keys-list-get#get-key [location]: https://cloud.google.com/compute/docs/regions-zones#available -[wave-docs]: https://www.nextflow.io/docs/latest/wave.html +[wave-docs]: https://docs.seqera.io/nextflow/wave [fusion-docs]: https://docs.seqera.io/fusion [platform-fusion-docs]: ../supported_software/fusion/overview [pre-post-run-scripts]: ../launch/advanced#pre-and-post-run-scripts diff --git a/platform-enterprise_versioned_docs/version-24.2/compute-envs/google-cloud-lifesciences.md b/platform-enterprise_versioned_docs/version-24.2/compute-envs/google-cloud-lifesciences.md index 10b33e087..256e80fdd 100644 --- a/platform-enterprise_versioned_docs/version-24.2/compute-envs/google-cloud-lifesciences.md +++ b/platform-enterprise_versioned_docs/version-24.2/compute-envs/google-cloud-lifesciences.md @@ -121,7 +121,7 @@ You can create multiple credentials in your Seqera workspace. See [Credentials]( 8. In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the region selected in the previous step. :::note - When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 9. You can enable **Preemptible** to use preemptible instances, which have significantly reduced cost compared to on-demand instances. diff --git a/platform-enterprise_versioned_docs/version-24.2/compute-envs/hpc.md b/platform-enterprise_versioned_docs/version-24.2/compute-envs/hpc.md index ed65646d1..26d35eb3a 100644 --- a/platform-enterprise_versioned_docs/version-24.2/compute-envs/hpc.md +++ b/platform-enterprise_versioned_docs/version-24.2/compute-envs/hpc.md @@ -19,7 +19,7 @@ To launch pipelines into an **HPC** cluster from Seqera, the following requireme - The cluster should allow outbound connections to the Seqera web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Credentials @@ -64,8 +64,8 @@ To create a new **HPC** compute environment: 1. Enter the absolute path of the **Launch directory** to be used on the cluster. If omitted, it will be the same as the work directory. 1. Enter the **Login hostname**. This is usually the hostname or public IP address of the cluster's login node. -1. Enter the **Head queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will be submitted. -1. Enter the **Compute queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will submit tasks. +1. Enter the **Head queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will be submitted. +1. Enter the **Compute queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will submit tasks. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. diff --git a/platform-enterprise_versioned_docs/version-24.2/compute-envs/overview.md b/platform-enterprise_versioned_docs/version-24.2/compute-envs/overview.md index 81a174b08..39202d2d1 100644 --- a/platform-enterprise_versioned_docs/version-24.2/compute-envs/overview.md +++ b/platform-enterprise_versioned_docs/version-24.2/compute-envs/overview.md @@ -47,8 +47,8 @@ Some important considerations: - Seqera only supports NVIDIA GPUs. Select instances with NVIDIA GPUs for your GPU-dependent processes. - The **Enable GPUs** setting causes Batch Forge to specify the most current [AWS-recommended GPU-optimized ECS AMI](https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ecs-optimized_AMI.html) as the EC2 fleet AMI when creating the compute environment. This setting can be overridden by **AMI ID** in the advanced options. - The **Enable GPUs** setting alone does not deploy GPU instances in your compute environment. You must still specify GPU-enabled instance types in the **Advanced options > Instance types** field. -- Your Nextflow script must include [accelerator directives](https://www.nextflow.io/docs/latest/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. -- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: +- Your Nextflow script must include [accelerator directives](https://docs.seqera.io/nextflow/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. +- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://docs.seqera.io/nextflow/process#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: ```groovy process { diff --git a/platform-enterprise_versioned_docs/version-24.2/credentials/aws_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.2/credentials/aws_registry_credentials.md index ee4ec636e..14c5b565a 100644 --- a/platform-enterprise_versioned_docs/version-24.2/credentials/aws_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.2/credentials/aws_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [aws, ecr, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-24.2/credentials/azure_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.2/credentials/azure_registry_credentials.md index 47e0184b7..a35a15b43 100644 --- a/platform-enterprise_versioned_docs/version-24.2/credentials/azure_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.2/credentials/azure_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [azure, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-24.2/credentials/docker_hub_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.2/credentials/docker_hub_registry_credentials.md index 1c1e376d6..8ce8339a4 100644 --- a/platform-enterprise_versioned_docs/version-24.2/credentials/docker_hub_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.2/credentials/docker_hub_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [docker, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-24.2/credentials/gitea_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.2/credentials/gitea_registry_credentials.md index 68942d36e..83f4668ed 100644 --- a/platform-enterprise_versioned_docs/version-24.2/credentials/gitea_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.2/credentials/gitea_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [gitea, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). Gitea container registries support [authentication][gitea-auth] using a personal access token. Use your personal access token as your password when you create your Gitea container registry credentials in Seqera. diff --git a/platform-enterprise_versioned_docs/version-24.2/credentials/github_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.2/credentials/github_registry_credentials.md index e69de52aa..f24937d55 100644 --- a/platform-enterprise_versioned_docs/version-24.2/credentials/github_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.2/credentials/github_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [github, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). GitHub Packages only supports [authentication][github-pat] using a personal access token (classic). Use your personal access token as your password when you create your GitHub container registry credentials in Seqera. diff --git a/platform-enterprise_versioned_docs/version-24.2/credentials/gitlab_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.2/credentials/gitlab_registry_credentials.md index 8a969ffbe..0acee7cc9 100644 --- a/platform-enterprise_versioned_docs/version-24.2/credentials/gitlab_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.2/credentials/gitlab_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [gitlab, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). If your organization enabled two-factor authentication (2FA) for your GitLab organization or project, you must use your [personal access token][gitlab-pat] as your password when you create your [GitLab container registry credentials][gitlab-cr]. diff --git a/platform-enterprise_versioned_docs/version-24.2/credentials/google_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.2/credentials/google_registry_credentials.md index 931f276bf..f95d8a434 100644 --- a/platform-enterprise_versioned_docs/version-24.2/credentials/google_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.2/credentials/google_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [google, container, registry, artifact, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-24.2/credentials/overview.md b/platform-enterprise_versioned_docs/version-24.2/credentials/overview.md index 6c45a55ae..5016f4eb4 100644 --- a/platform-enterprise_versioned_docs/version-24.2/credentials/overview.md +++ b/platform-enterprise_versioned_docs/version-24.2/credentials/overview.md @@ -7,7 +7,7 @@ tags: [credentials] Configure **workspace credentials** in Seqera Platform to store the access keys and tokens for your [compute environments](../compute-envs/overview) and [Git hosting services](../git/overview). -From version 22.3, you can configure **container registry credentials** to be used by the [Wave container service](https://nextflow.io/docs/latest/wave.html) to authenticate to private and public container registries like Docker Hub, Google Artifact Registry, Quay, etc. +From version 22.3, you can configure **container registry credentials** to be used by the [Wave container service](https://docs.seqera.io/nextflow/wave) to authenticate to private and public container registries like Docker Hub, Google Artifact Registry, Quay, etc. See the **Container registry credentials** section for registry-specific instructions. diff --git a/platform-enterprise_versioned_docs/version-24.2/credentials/quay_registry_credentials.md b/platform-enterprise_versioned_docs/version-24.2/credentials/quay_registry_credentials.md index 9a160b73d..93563fa32 100644 --- a/platform-enterprise_versioned_docs/version-24.2/credentials/quay_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-24.2/credentials/quay_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [quay, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-24.2/enterprise/advanced-topics/manual-azure-batch-setup.md b/platform-enterprise_versioned_docs/version-24.2/enterprise/advanced-topics/manual-azure-batch-setup.md index 598419799..b6a4da3fb 100644 --- a/platform-enterprise_versioned_docs/version-24.2/enterprise/advanced-topics/manual-azure-batch-setup.md +++ b/platform-enterprise_versioned_docs/version-24.2/enterprise/advanced-topics/manual-azure-batch-setup.md @@ -268,7 +268,7 @@ Select **Launch** next to the `hello-world-autopool` pipeline in your workspace Seqera can utilize an Azure Entra service principal to authenticate and access Azure Batch for job execution and Azure Storage for data management, and Nextflow can authenticate to Azure services using a managed identity. This method offers enhanced security compared to access keys, but must run on Azure infrastructure. -See [Microsoft Entra](https://www.nextflow.io/docs/latest/azure.html#microsoft-entra) in the Nextflow documentation for more information. +See [Microsoft Entra](https://docs.seqera.io/nextflow/azure#microsoft-entra) in the Nextflow documentation for more information. #### Create a service principal for Seqera to use for authentication @@ -288,7 +288,7 @@ In Seqera: Back in the Azure Portal: 1. [Create a managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-manage-user-assigned-managed-identities?pivots=identity-mi-methods-azp) -1. [Assign the relevant roles to the managed identity](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current). See [Required role assignments](https://www.nextflow.io/docs/latest/azure.html#required-role-assignments) for Nextflow requirements. +1. [Assign the relevant roles to the managed identity](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current). See [Required role assignments](https://docs.seqera.io/nextflow/azure#required-role-assignments) for Nextflow requirements. 1. Note the managed identity client ID for later. 1. In the Azure Portal, go to the Batch account you created earlier. 1. Go to the **Pools** tab and find the pool called `tower-pool-${id}`, where `${id}` is the ID of the head node pool created earlier. @@ -429,6 +429,6 @@ If you wish to keep the Azure resources, you can remove each pool within a Batch [install-azure-cli]: https://learn.microsoft.com/en-us/cli/azure/install-azure-cli [install-seqera-cli]: /platform-cli/installation -[nextflow-working-directory]: https://www.nextflow.io/docs/latest/cache-and-resume.html#work-directory +[nextflow-working-directory]: https://docs.seqera.io/nextflow/cache-and-resume#work-directory [create-org-workspace]: ../../getting-started/workspace-setup [add-pipeline]: ../../getting-started/quickstart-demo/add-pipelines#add-from-the-launchpad diff --git a/platform-enterprise_versioned_docs/version-24.2/enterprise/configuration/wave.md b/platform-enterprise_versioned_docs/version-24.2/enterprise/configuration/wave.md index 50e810a27..1a8244f57 100644 --- a/platform-enterprise_versioned_docs/version-24.2/enterprise/configuration/wave.md +++ b/platform-enterprise_versioned_docs/version-24.2/enterprise/configuration/wave.md @@ -7,7 +7,7 @@ tags: [wave, containers, configuration] From version 22.4, Seqera Platform Enterprise supports the Seqera Wave containers service for on-prem installations. -To learn more about Wave, see [Wave containers](https://wave.seqera.io). To learn more about Wave and Nextflow integration, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +To learn more about Wave, see [Wave containers](https://wave.seqera.io). To learn more about Wave and Nextflow integration, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). ## Pair your Seqera instance with Wave @@ -35,4 +35,4 @@ When these conditions are met, the Wave feature is available on the Seqera compu After Wave is enabled, you can use private container repositories and the Fusion file system in your Nextflow pipelines. -Wave can also be enabled in the Nextflow pipeline config file. See the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html) for more information. +Wave can also be enabled in the Nextflow pipeline config file. See the [Nextflow documentation](https://docs.seqera.io/nextflow/wave) for more information. diff --git a/platform-enterprise_versioned_docs/version-24.2/getting-started/deployment-options.md b/platform-enterprise_versioned_docs/version-24.2/getting-started/deployment-options.md index 304ffb33b..c0568990d 100644 --- a/platform-enterprise_versioned_docs/version-24.2/getting-started/deployment-options.md +++ b/platform-enterprise_versioned_docs/version-24.2/getting-started/deployment-options.md @@ -96,5 +96,5 @@ If you have an existing environment where you run Nextflow directly, you can sti You can now monitor your workflow runs in the Seqera interface. To configure and execute Nextflow pipelines in cloud environments, see [compute environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-enterprise_versioned_docs/version-24.2/getting-started/proteinfold.mdx b/platform-enterprise_versioned_docs/version-24.2/getting-started/proteinfold.mdx index c60acc853..267a01db8 100644 --- a/platform-enterprise_versioned_docs/version-24.2/getting-started/proteinfold.mdx +++ b/platform-enterprise_versioned_docs/version-24.2/getting-started/proteinfold.mdx @@ -187,7 +187,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL: `https://github.com/nf-core/proteinfold`. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name: `1.1.1`. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-enterprise_versioned_docs/version-24.2/getting-started/quickstart-demo/launch-pipelines.md b/platform-enterprise_versioned_docs/version-24.2/getting-started/quickstart-demo/launch-pipelines.md index e33272298..5eab76c65 100644 --- a/platform-enterprise_versioned_docs/version-24.2/getting-started/quickstart-demo/launch-pipelines.md +++ b/platform-enterprise_versioned_docs/version-24.2/getting-started/quickstart-demo/launch-pipelines.md @@ -44,7 +44,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- (*Optional*) **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. +- (*Optional*) **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - (*Optional*) **Labels**: Assign new or existing [labels](../../labels/overview) to the run. - **Compute environment**: Select an existing workspace [compute environment](../../compute-envs/overview). diff --git a/platform-enterprise_versioned_docs/version-24.2/getting-started/rnaseq.mdx b/platform-enterprise_versioned_docs/version-24.2/getting-started/rnaseq.mdx index e6ba8371b..1f8ee2bc3 100644 --- a/platform-enterprise_versioned_docs/version-24.2/getting-started/rnaseq.mdx +++ b/platform-enterprise_versioned_docs/version-24.2/getting-started/rnaseq.mdx @@ -199,7 +199,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-enterprise_versioned_docs/version-24.2/launch/advanced.md b/platform-enterprise_versioned_docs/version-24.2/launch/advanced.md index 35c223dc7..c05b2a5c8 100644 --- a/platform-enterprise_versioned_docs/version-24.2/launch/advanced.md +++ b/platform-enterprise_versioned_docs/version-24.2/launch/advanced.md @@ -9,7 +9,7 @@ You can modify the configuration and execution of a pipeline with advanced launc ### Nextflow config file -Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://www.nextflow.io/docs/latest/config.html#config-syntax). +Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax). For example, modify the **manifest** section to give the pipeline a name and description that will show up in the Seqera monitoring section: @@ -106,7 +106,7 @@ Instruct Nextflow to pull the latest pipeline version from the Git repository. T ### Stub run -Replace Nextflow process commands with command [stubs](https://www.nextflow.io/docs/latest/process.html#stub), where defined, before execution. +Replace Nextflow process commands with command [stubs](https://docs.seqera.io/nextflow/process#stub), where defined, before execution. ### Main script diff --git a/platform-enterprise_versioned_docs/version-24.2/launch/cache-resume.mdx b/platform-enterprise_versioned_docs/version-24.2/launch/cache-resume.mdx index 558b0d2ad..ef47bd4d2 100644 --- a/platform-enterprise_versioned_docs/version-24.2/launch/cache-resume.mdx +++ b/platform-enterprise_versioned_docs/version-24.2/launch/cache-resume.mdx @@ -8,13 +8,13 @@ tags: [cache, launch, resume, relaunch] import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; -Nextflow maintains a [cache](https://www.nextflow.io/docs/latest/cache-and-resume.html) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. +Nextflow maintains a [cache](https://docs.seqera.io/nextflow/cache-and-resume) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. ## Cache directory -Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. +Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. -To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://www.nextflow.io/docs/latest/process.html#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). +To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://docs.seqera.io/nextflow/process#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). @@ -108,7 +108,7 @@ Kubernetes compute environments do not use cloud cache by default. To specify a Google Cloud Storage 1. See [these instructions](../compute-envs/google-cloud-batch#iam) to set up IAM and create a JSON key file for the custom service account with permissions to your Google Cloud storage account. - 2. If you run the [gcloud CLI authentication flow](https://nextflow.io/docs/edge/google.html#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. + 2. If you run the [gcloud CLI authentication flow](https://docs.seqera.io/nextflow/google#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. 3. Add the following to the **Nextflow Config file** field when you [launch](../launch/launchpad#launch-form) your pipeline: ```groovy diff --git a/platform-enterprise_versioned_docs/version-24.2/launch/launchpad.md b/platform-enterprise_versioned_docs/version-24.2/launch/launchpad.md index 22530a830..cabaa2aa0 100644 --- a/platform-enterprise_versioned_docs/version-24.2/launch/launchpad.md +++ b/platform-enterprise_versioned_docs/version-24.2/launch/launchpad.md @@ -35,10 +35,10 @@ For saved pipelines, **General config** and **Run parameters** fields are prefil - **Pipeline to launch**: A Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. Private repositories require [access credentials](../credentials/overview). :::note - Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://www.nextflow.io/docs/latest/sharing.html) in the Nextflow docs for more details. + Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://docs.seqera.io/nextflow/sharing) in the Nextflow docs for more details. ::: - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: A unique identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: The [compute environment](../compute-envs/overview) where the run will be launched. @@ -112,7 +112,7 @@ Use resource labels to tag the computing resources created during the workflow e Secrets are used to store keys and tokens used by workflow tasks to interact with external systems. Enter the names of any stored user or workspace secrets required for the workflow execution. :::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: #### Advanced options diff --git a/platform-enterprise_versioned_docs/version-24.2/monitoring/overview.md b/platform-enterprise_versioned_docs/version-24.2/monitoring/overview.md index 8a35cf2d3..0c04d617d 100644 --- a/platform-enterprise_versioned_docs/version-24.2/monitoring/overview.md +++ b/platform-enterprise_versioned_docs/version-24.2/monitoring/overview.md @@ -12,7 +12,7 @@ The **Runs** tab contains all previous runs in the workspace. Each new or resume - `submitted`: Pending execution - `running`: Running - `succeeded`: Completed successfully -- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://www.nextflow.io/docs/latest/process.html#errorstrategy) +- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://docs.seqera.io/nextflow/process#errorstrategy) - `cancelled`: Stopped manually during execution - `unknown`: Indeterminate status diff --git a/platform-enterprise_versioned_docs/version-24.2/platform-enterprise.md b/platform-enterprise_versioned_docs/version-24.2/platform-enterprise.md index fe4b9c7cd..33a186eca 100644 --- a/platform-enterprise_versioned_docs/version-24.2/platform-enterprise.md +++ b/platform-enterprise_versioned_docs/version-24.2/platform-enterprise.md @@ -28,4 +28,4 @@ Request a [**demo**](https://seqera.io/demo "Seqera Enterprise Demo") to explore Nextflow is both a programming workflow language and an execution runtime that supports a wide range of execution platforms, including popular traditional grid scheduling systems such as Slurm and IBM LSF, and cloud services such as AWS, Azure, and Google Cloud Batch. -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/) to learn more. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/) to learn more. diff --git a/platform-enterprise_versioned_docs/version-24.2/reports/overview.md b/platform-enterprise_versioned_docs/version-24.2/reports/overview.md index c4ba99b1c..59db26855 100644 --- a/platform-enterprise_versioned_docs/version-24.2/reports/overview.md +++ b/platform-enterprise_versioned_docs/version-24.2/reports/overview.md @@ -82,10 +82,10 @@ By default, the MIME type is deduced from the file extension, so you don't need Nextflow can generate a number of built-in reports: -- [Execution report](https://nextflow.io/docs/latest/tracing.html#execution-report) -- [Execution timeline](https://nextflow.io/docs/latest/tracing.html#timeline-report) -- [Trace file](https://nextflow.io/docs/latest/tracing.html#trace-report) -- [Workflow diagram](https://nextflow.io/docs/latest/tracing.html#dag-visualisation) (i.e. DAG) +- [Execution report](https://docs.seqera.io/nextflow/tracing#execution-report) +- [Execution timeline](https://docs.seqera.io/nextflow/tracing#timeline-report) +- [Trace file](https://docs.seqera.io/nextflow/tracing#trace-report) +- [Workflow diagram](https://docs.seqera.io/nextflow/tracing#dag-visualisation) (i.e. DAG) In Nextflow version 24.03.0-edge and later, these reports can be included as pipeline reports in Seqera Platform. Specify them in `tower.yml` like any other file: diff --git a/platform-enterprise_versioned_docs/version-24.2/secrets/overview.md b/platform-enterprise_versioned_docs/version-24.2/secrets/overview.md index 7ba61f4ee..5d7c02330 100644 --- a/platform-enterprise_versioned_docs/version-24.2/secrets/overview.md +++ b/platform-enterprise_versioned_docs/version-24.2/secrets/overview.md @@ -31,12 +31,12 @@ Secrets defined by a user have higher priority and will override any secrets wit ## Use secrets in workflows -When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://www.nextflow.io/docs/edge/secrets.html#process-secrets) for more information. +When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://docs.seqera.io/nextflow/secrets) for more information. Secrets are automatically deleted from the secret manager when the pipeline completes, successfully or unsuccessfully. -:::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +:::note +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: ## AWS Secrets Manager integration diff --git a/platform-enterprise_versioned_docs/version-24.2/supported_software/dragen/overview.md b/platform-enterprise_versioned_docs/version-24.2/supported_software/dragen/overview.md index 7eaf0d4d4..1bbdb4833 100644 --- a/platform-enterprise_versioned_docs/version-24.2/supported_software/dragen/overview.md +++ b/platform-enterprise_versioned_docs/version-24.2/supported_software/dragen/overview.md @@ -57,7 +57,7 @@ See the [dragen.nf](https://github.com/seqeralabs/nf-dragen/blob/master/modules/ } ``` - See the [Nextflow label docs](https://www.nextflow.io/docs/latest/process.html?highlight=label#label) for more information. + See the [Nextflow label docs](https://docs.seqera.io/nextflow/process.html?highlight=label#label) for more information. 2. Define secrets in Seqera: diff --git a/platform-enterprise_versioned_docs/version-24.2/troubleshooting_and_faqs/azure_troubleshooting.md b/platform-enterprise_versioned_docs/version-24.2/troubleshooting_and_faqs/azure_troubleshooting.md index 9ce13e2e8..3c2430d43 100644 --- a/platform-enterprise_versioned_docs/version-24.2/troubleshooting_and_faqs/azure_troubleshooting.md +++ b/platform-enterprise_versioned_docs/version-24.2/troubleshooting_and_faqs/azure_troubleshooting.md @@ -20,12 +20,12 @@ The default Azure Batch implementation in Seqera Platform uses a single pool for - One [Low priority](https://learn.microsoft.com/en-us/azure/batch/batch-spot-vms#differences-between-spot-and-low-priority-vms) :::note -Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://www.nextflow.io/docs/latest/azure.html#requirements-on-pre-existing-named-pools). +Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://docs.seqera.io/nextflow/azure#requirements-on-pre-existing-named-pools). ::: 2. Create a manual [Azure Batch](../compute-envs/azure-batch#manual) compute environment in Seqera Platform. 3. In **Compute pool name**, specify your dedicated Batch pool. -4. Specify the Low priority pool using the `process.queue` [directive](https://www.nextflow.io/docs/latest/process.html#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. +4. Specify the Low priority pool using the `process.queue` [directive](https://docs.seqera.io/nextflow/process#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. ### Azure Kubernetes Service (AKS) diff --git a/platform-enterprise_versioned_docs/version-24.2/troubleshooting_and_faqs/nextflow.md b/platform-enterprise_versioned_docs/version-24.2/troubleshooting_and_faqs/nextflow.md index 114f25ec2..8b9c3d97c 100644 --- a/platform-enterprise_versioned_docs/version-24.2/troubleshooting_and_faqs/nextflow.md +++ b/platform-enterprise_versioned_docs/version-24.2/troubleshooting_and_faqs/nextflow.md @@ -19,7 +19,7 @@ To minimize disruption on existing pipelines, version 22.1.x and later are confi **Invoke Nextflow CLI run arguments during Seqera launch** -From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://www.nextflow.io/docs/latest/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): +From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://docs.seqera.io/nextflow/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): ``` export NXF_CLI_OPTS='-dump-hashes' @@ -43,7 +43,7 @@ Currently, you can resolve this by creating empty `main.nf` and `nextflow.config **Use multiple Nextflow configuration files for different environments** -The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) in the main `nextflow.config`. +The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://docs.seqera.io/nextflow/config#config-profiles) in the main `nextflow.config`. Example: @@ -151,7 +151,7 @@ process.afterScript = 'sleep 60' **Jobs remain in RUNNING status when a pipeline run is canceled** -Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: +Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://docs.seqera.io/nextflow/process#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: ``` process terminateError { @@ -195,7 +195,7 @@ The Groovy shell used by Nextflow to execute your workflow has a hard limit on s 1. Remove any unnecessary code or comments from the script. 2. Move long script bodies into a separate script file in the pipeline `/bin` directory. -3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://www.nextflow.io/docs/latest/dsl2.html#modules). +3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://docs.seqera.io/nextflow/dsl2#modules). ### Nextflow Launcher @@ -225,4 +225,4 @@ If you rely on silent Spot retries (the previous default behavior), you may now - **AWS**: Generic failure with `exit code 1`. You may see messages indicating the host machine was terminated. - **Google**: Spot reclamation typically produces a specific code, but is now surfaced as a recognizable task failure in Nextflow logs. -Since the default for Spot retries is now zero, you must actively enable a retry strategy if you want Nextflow to handle reclaimed Spot instances automatically. For more information, see the [Spot Instance failures and retries](https://www.nextflow.io/docs/latest/updating-spot-retries.html) guide. +Since the default for Spot retries is now zero, you must actively enable a retry strategy if you want Nextflow to handle reclaimed Spot instances automatically. For more information, see the [Spot Instance failures and retries](https://docs.seqera.io/nextflow/updating-spot-retries) guide. diff --git a/platform-enterprise_versioned_docs/version-24.2/troubleshooting_and_faqs/troubleshooting.md b/platform-enterprise_versioned_docs/version-24.2/troubleshooting_and_faqs/troubleshooting.md index e2b833ce2..b831111dc 100644 --- a/platform-enterprise_versioned_docs/version-24.2/troubleshooting_and_faqs/troubleshooting.md +++ b/platform-enterprise_versioned_docs/version-24.2/troubleshooting_and_faqs/troubleshooting.md @@ -43,7 +43,7 @@ This error can occur if you execute a DSL1-based Nextflow workflow using [Nextfl The `sleep` commands in your Nextflow workflows may differ in behavior depending on where they are: - If used within an `errorStrategy` block, the Groovy sleep function will be used (which takes its value in milliseconds). -- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://www.nextflow.io/docs/latest/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. +- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://docs.seqera.io/nextflow/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. **Large number of batch job definitions** diff --git a/platform-enterprise_versioned_docs/version-25.1/compute-envs/aws-batch.md b/platform-enterprise_versioned_docs/version-25.1/compute-envs/aws-batch.md index f0e207873..a0e93594e 100644 --- a/platform-enterprise_versioned_docs/version-25.1/compute-envs/aws-batch.md +++ b/platform-enterprise_versioned_docs/version-25.1/compute-envs/aws-batch.md @@ -686,7 +686,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM 1. In the **Pipeline work directory** field type or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation), e.g., `s3://seqera-bucket`. The work directory can be customized to specify a folder inside the bucket where Nextflow intermediate files will be stored, e.g., `s3://seqera-bucket/nextflow-workdir`. The bucket must be located in the same region chosen in the previous step. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -695,7 +695,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM Using an EFS or FSx file system as your work directory is currently incompatible with [Studios](../studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
@@ -918,7 +918,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See 1. Select a **Region**, e.g., _eu-west-1 - Europe (Ireland)_. This region must match the region where your S3 bucket or EFS/FSx work directory is located to avoid high data transfer costs. 1. Enter or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation) in the **Pipeline work directory** field, e.g., `s3://seqera-bucket`. This bucket must be in the same region chosen in the previous step to avoid incurring high data transfer costs. The work directory can be customized to specify a folder inside the bucket, e.g., `s3://seqera-bucket/nextflow-workdir`. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -927,7 +927,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See Using an EFS or FSx file system as your work directory is currently incompatible with [Studios](../studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
diff --git a/platform-enterprise_versioned_docs/version-25.1/compute-envs/azure-batch.md b/platform-enterprise_versioned_docs/version-25.1/compute-envs/azure-batch.md index cd14c96dd..7435c6ebf 100644 --- a/platform-enterprise_versioned_docs/version-25.1/compute-envs/azure-batch.md +++ b/platform-enterprise_versioned_docs/version-25.1/compute-envs/azure-batch.md @@ -189,7 +189,7 @@ Nextflow can authenticate to Azure services using a managed identity. This metho When you use a manually-configured compute environment with a managed identity attached to the Azure Batch Pool, Nextflow can use this managed identity for authentication. However, Seqera still needs to use access keys or an Entra service principal to submit the initial task to Azure Batch to run Nextflow, which will then proceed with the managed identity for subsequent authentication. 1. In Azure, create a user-assigned managed identity. See [Manage user-assigned managed identities](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-manage-user-assigned-managed-identities) for detailed steps. Take note of the client ID of the managed identity when you create it. -1. The user-assigned managed identity must have the necessary access roles for Nextflow. See [Required role assignments](https://www.nextflow.io/docs/latest/azure.html#required-role-assignments) for more information. +1. The user-assigned managed identity must have the necessary access roles for Nextflow. See [Required role assignments](https://docs.seqera.io/nextflow/azure#required-role-assignments) for more information. 1. Associate the user-assigned managed identity with the Azure Batch Pool. See [Set up managed identity in your Batch pool](https://learn.microsoft.com/en-us/troubleshoot/azure/hpc/batch/use-managed-identities-azure-batch-account-pool#set-up-managed-identity-in-your-batch-pool) for more information. 1. When you set up the Seqera compute environment, select the Azure Batch pool by name and enter the managed identity client ID in the specified field as instructed above. @@ -252,7 +252,7 @@ Create a Batch Forge Azure Batch compute environment: 1. Select a **Region**, such as _eastus_. 1. In the **Pipeline work directory** field, enter the Azure blob container created previously. For example, `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. 1. Select **Enable Fusion v2** to allow access to your Azure Blob Storage data via the [Fusion v2][fusion-docs] virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. @@ -285,7 +285,7 @@ Create a Batch Forge Azure Batch compute environment: 1. Enter the **VMs count**. If autoscaling is enabled (default), this is the maximum number of VMs you wish the pool to scale up to. If autoscaling is disabled, this is the fixed number of virtual machines in the pool. 1. Enable **Autoscale** to scale up and down automatically, based on the number of pipeline tasks. The number of VMs will vary from **0** to **VMs count**. 1. Enable **Dispose resources** for Seqera to automatically delete the Batch pool if the compute environment is deleted on the platform. -1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://www.nextflow.io/docs/latest/wave.html) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. +1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://docs.seqera.io/nextflow/wave) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. 1. Apply [**Resource labels**](../resource-labels/overview). This will populate the **Metadata** fields of the Azure Batch pool. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. @@ -396,7 +396,7 @@ The following settings can be modified after creating a pool: 1. Select a **Region**, such as _eastus (East US)_. 1. In the **Pipeline work directory** field, add the Azure blob container created previously. For example, `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. 1. Select **Enable Fusion v2** to allow access to your Azure Blob Storage data via the [Fusion v2][fusion-docs] virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. @@ -463,7 +463,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [az-vm-gen]: https://learn.microsoft.com/en-us/azure/virtual-machines/generation-2 [az-disk-type]: https://learn.microsoft.com/en-us/azure/virtual-machines/disks-types [az-batch-autoscale]: https://learn.microsoft.com/en-us/azure/batch/batch-automatic-scaling -[az-file-shares]: https://www.nextflow.io/docs/latest/azure.html#azure-file-shares +[az-file-shares]: https://docs.seqera.io/nextflow/azure#azure-file-shares [az-vm-sizes]: https://learn.microsoft.com/en-us/azure/virtual-machines/sizes/overview [wave-docs]: https://docs.seqera.io/wave diff --git a/platform-enterprise_versioned_docs/version-25.1/compute-envs/google-cloud-batch.md b/platform-enterprise_versioned_docs/version-25.1/compute-envs/google-cloud-batch.md index d277a835e..4fd7c8c49 100644 --- a/platform-enterprise_versioned_docs/version-25.1/compute-envs/google-cloud-batch.md +++ b/platform-enterprise_versioned_docs/version-25.1/compute-envs/google-cloud-batch.md @@ -147,7 +147,7 @@ Select the **Location** where you will execute your pipelines. See [Location][lo In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the location selected in the previous step. :::note -When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. +When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: #### Seqera features @@ -171,7 +171,7 @@ Select **Enable Fusion v2** to allow access to your Google Cloud Storage data vi :::note To specify virtual machine settings in Platform during compute environment creation, use the **Global Nextflow config** field to apply custom Nextflow process directives to all pipeline runs launched with this compute environment. - To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://www.nextflow.io/docs/latest/google.html#process-definition) for more information. + To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://docs.seqera.io/nextflow/google#process-definition) for more information. ::: When Fusion v2 is enabled, the following virtual machine settings are applied: @@ -231,7 +231,7 @@ If you use VM instance templates for the head or compute jobs (see step 6 below) :::caution Seqera does not validate the VM instance template you specify in these fields. Generally, use templates that define only the machine type, network, disk, and configuration values that will not change across multiple VM instances and Seqera compute environments. See [Create instance templates](https://cloud.google.com/compute/docs/instance-templates/create-instance-templates) for instructions to create your instance templates. - To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://www.nextflow.io/docs/latest/google.html#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://www.nextflow.io/docs/latest/config.html#config-process-selectors) to assign separate templates to each of your processes. + To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://docs.seqera.io/nextflow/google#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://docs.seqera.io/nextflow/config#config-process-selectors) to assign separate templates to each of your processes. ::: Select **Create** to finalize the compute environment setup. @@ -244,7 +244,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [create-sa]: https://cloud.google.com/iam/docs/service-accounts-create#creating [get-json]: https://cloud.google.com/iam/docs/keys-list-get#get-key [location]: https://cloud.google.com/compute/docs/regions-zones#available -[wave-docs]: https://www.nextflow.io/docs/latest/wave.html +[wave-docs]: https://docs.seqera.io/nextflow/wave [fusion-docs]: https://docs.seqera.io/fusion [platform-fusion-docs]: ../supported_software/fusion/overview [pre-post-run-scripts]: ../launch/advanced#pre-and-post-run-scripts diff --git a/platform-enterprise_versioned_docs/version-25.1/compute-envs/google-cloud-lifesciences.md b/platform-enterprise_versioned_docs/version-25.1/compute-envs/google-cloud-lifesciences.md index 11e2a2e68..49313fd23 100644 --- a/platform-enterprise_versioned_docs/version-25.1/compute-envs/google-cloud-lifesciences.md +++ b/platform-enterprise_versioned_docs/version-25.1/compute-envs/google-cloud-lifesciences.md @@ -121,7 +121,7 @@ You can create multiple credentials in your Seqera workspace. See [Credentials]( 8. In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the region selected in the previous step. :::note - When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 9. You can enable **Preemptible** to use preemptible instances, which have significantly reduced cost compared to on-demand instances. diff --git a/platform-enterprise_versioned_docs/version-25.1/compute-envs/hpc.md b/platform-enterprise_versioned_docs/version-25.1/compute-envs/hpc.md index ed65646d1..26d35eb3a 100644 --- a/platform-enterprise_versioned_docs/version-25.1/compute-envs/hpc.md +++ b/platform-enterprise_versioned_docs/version-25.1/compute-envs/hpc.md @@ -19,7 +19,7 @@ To launch pipelines into an **HPC** cluster from Seqera, the following requireme - The cluster should allow outbound connections to the Seqera web service. - The cluster queue used to run the Nextflow head job must be able to submit cluster jobs. -- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://nextflow.io/docs/latest/install.html). +- The Nextflow runtime version **21.02.0-edge** (or later) must be [installed on the cluster](https://docs.seqera.io/nextflow/install). ## Credentials @@ -64,8 +64,8 @@ To create a new **HPC** compute environment: 1. Enter the absolute path of the **Launch directory** to be used on the cluster. If omitted, it will be the same as the work directory. 1. Enter the **Login hostname**. This is usually the hostname or public IP address of the cluster's login node. -1. Enter the **Head queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will be submitted. -1. Enter the **Compute queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will submit tasks. +1. Enter the **Head queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will be submitted. +1. Enter the **Compute queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will submit tasks. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. diff --git a/platform-enterprise_versioned_docs/version-25.1/compute-envs/overview.md b/platform-enterprise_versioned_docs/version-25.1/compute-envs/overview.md index 3e12d1833..19765bccf 100644 --- a/platform-enterprise_versioned_docs/version-25.1/compute-envs/overview.md +++ b/platform-enterprise_versioned_docs/version-25.1/compute-envs/overview.md @@ -47,8 +47,8 @@ Some important considerations: - Seqera only supports NVIDIA GPUs. Select instances with NVIDIA GPUs for your GPU-dependent processes. - The **Enable GPUs** setting causes Batch Forge to specify the most current [AWS-recommended GPU-optimized ECS AMI](https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ecs-optimized_AMI.html) as the EC2 fleet AMI when creating the compute environment. This setting can be overridden by **AMI ID** in the advanced options. - The **Enable GPUs** setting alone does not deploy GPU instances in your compute environment. You must still specify GPU-enabled instance types in the **Advanced options > Instance types** field. -- Your Nextflow script must include [accelerator directives](https://www.nextflow.io/docs/latest/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. -- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: +- Your Nextflow script must include [accelerator directives](https://docs.seqera.io/nextflow/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. +- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://docs.seqera.io/nextflow/process#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: ```groovy process { diff --git a/platform-enterprise_versioned_docs/version-25.1/credentials/aws_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.1/credentials/aws_registry_credentials.md index 337f109ec..15f17af93 100644 --- a/platform-enterprise_versioned_docs/version-25.1/credentials/aws_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.1/credentials/aws_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [aws, ecr, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-25.1/credentials/azure_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.1/credentials/azure_registry_credentials.md index 47e0184b7..a35a15b43 100644 --- a/platform-enterprise_versioned_docs/version-25.1/credentials/azure_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.1/credentials/azure_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [azure, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-25.1/credentials/docker_hub_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.1/credentials/docker_hub_registry_credentials.md index 1c1e376d6..8ce8339a4 100644 --- a/platform-enterprise_versioned_docs/version-25.1/credentials/docker_hub_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.1/credentials/docker_hub_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [docker, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-25.1/credentials/gitea_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.1/credentials/gitea_registry_credentials.md index 68942d36e..83f4668ed 100644 --- a/platform-enterprise_versioned_docs/version-25.1/credentials/gitea_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.1/credentials/gitea_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [gitea, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). Gitea container registries support [authentication][gitea-auth] using a personal access token. Use your personal access token as your password when you create your Gitea container registry credentials in Seqera. diff --git a/platform-enterprise_versioned_docs/version-25.1/credentials/github_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.1/credentials/github_registry_credentials.md index e69de52aa..f24937d55 100644 --- a/platform-enterprise_versioned_docs/version-25.1/credentials/github_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.1/credentials/github_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [github, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). GitHub Packages only supports [authentication][github-pat] using a personal access token (classic). Use your personal access token as your password when you create your GitHub container registry credentials in Seqera. diff --git a/platform-enterprise_versioned_docs/version-25.1/credentials/gitlab_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.1/credentials/gitlab_registry_credentials.md index 8a969ffbe..0acee7cc9 100644 --- a/platform-enterprise_versioned_docs/version-25.1/credentials/gitlab_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.1/credentials/gitlab_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [gitlab, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). If your organization enabled two-factor authentication (2FA) for your GitLab organization or project, you must use your [personal access token][gitlab-pat] as your password when you create your [GitLab container registry credentials][gitlab-cr]. diff --git a/platform-enterprise_versioned_docs/version-25.1/credentials/google_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.1/credentials/google_registry_credentials.md index 931f276bf..f95d8a434 100644 --- a/platform-enterprise_versioned_docs/version-25.1/credentials/google_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.1/credentials/google_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [google, container, registry, artifact, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-25.1/credentials/overview.md b/platform-enterprise_versioned_docs/version-25.1/credentials/overview.md index 6c45a55ae..5016f4eb4 100644 --- a/platform-enterprise_versioned_docs/version-25.1/credentials/overview.md +++ b/platform-enterprise_versioned_docs/version-25.1/credentials/overview.md @@ -7,7 +7,7 @@ tags: [credentials] Configure **workspace credentials** in Seqera Platform to store the access keys and tokens for your [compute environments](../compute-envs/overview) and [Git hosting services](../git/overview). -From version 22.3, you can configure **container registry credentials** to be used by the [Wave container service](https://nextflow.io/docs/latest/wave.html) to authenticate to private and public container registries like Docker Hub, Google Artifact Registry, Quay, etc. +From version 22.3, you can configure **container registry credentials** to be used by the [Wave container service](https://docs.seqera.io/nextflow/wave) to authenticate to private and public container registries like Docker Hub, Google Artifact Registry, Quay, etc. See the **Container registry credentials** section for registry-specific instructions. diff --git a/platform-enterprise_versioned_docs/version-25.1/credentials/quay_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.1/credentials/quay_registry_credentials.md index 9a160b73d..93563fa32 100644 --- a/platform-enterprise_versioned_docs/version-25.1/credentials/quay_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.1/credentials/quay_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [quay, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-25.1/enterprise/advanced-topics/manual-azure-batch-setup.md b/platform-enterprise_versioned_docs/version-25.1/enterprise/advanced-topics/manual-azure-batch-setup.md index 598419799..b6a4da3fb 100644 --- a/platform-enterprise_versioned_docs/version-25.1/enterprise/advanced-topics/manual-azure-batch-setup.md +++ b/platform-enterprise_versioned_docs/version-25.1/enterprise/advanced-topics/manual-azure-batch-setup.md @@ -268,7 +268,7 @@ Select **Launch** next to the `hello-world-autopool` pipeline in your workspace Seqera can utilize an Azure Entra service principal to authenticate and access Azure Batch for job execution and Azure Storage for data management, and Nextflow can authenticate to Azure services using a managed identity. This method offers enhanced security compared to access keys, but must run on Azure infrastructure. -See [Microsoft Entra](https://www.nextflow.io/docs/latest/azure.html#microsoft-entra) in the Nextflow documentation for more information. +See [Microsoft Entra](https://docs.seqera.io/nextflow/azure#microsoft-entra) in the Nextflow documentation for more information. #### Create a service principal for Seqera to use for authentication @@ -288,7 +288,7 @@ In Seqera: Back in the Azure Portal: 1. [Create a managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-manage-user-assigned-managed-identities?pivots=identity-mi-methods-azp) -1. [Assign the relevant roles to the managed identity](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current). See [Required role assignments](https://www.nextflow.io/docs/latest/azure.html#required-role-assignments) for Nextflow requirements. +1. [Assign the relevant roles to the managed identity](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current). See [Required role assignments](https://docs.seqera.io/nextflow/azure#required-role-assignments) for Nextflow requirements. 1. Note the managed identity client ID for later. 1. In the Azure Portal, go to the Batch account you created earlier. 1. Go to the **Pools** tab and find the pool called `tower-pool-${id}`, where `${id}` is the ID of the head node pool created earlier. @@ -429,6 +429,6 @@ If you wish to keep the Azure resources, you can remove each pool within a Batch [install-azure-cli]: https://learn.microsoft.com/en-us/cli/azure/install-azure-cli [install-seqera-cli]: /platform-cli/installation -[nextflow-working-directory]: https://www.nextflow.io/docs/latest/cache-and-resume.html#work-directory +[nextflow-working-directory]: https://docs.seqera.io/nextflow/cache-and-resume#work-directory [create-org-workspace]: ../../getting-started/workspace-setup [add-pipeline]: ../../getting-started/quickstart-demo/add-pipelines#add-from-the-launchpad diff --git a/platform-enterprise_versioned_docs/version-25.1/enterprise/configuration/wave.md b/platform-enterprise_versioned_docs/version-25.1/enterprise/configuration/wave.md index b84fe0534..8d84565f1 100644 --- a/platform-enterprise_versioned_docs/version-25.1/enterprise/configuration/wave.md +++ b/platform-enterprise_versioned_docs/version-25.1/enterprise/configuration/wave.md @@ -79,5 +79,5 @@ See the [Wave documentation](https://docs.seqera.io/wave) for installation and c ## Additional resources - [Wave documentation](https://docs.seqera.io/wave) -- [Nextflow Wave integration](https://www.nextflow.io/docs/latest/wave.html) +- [Nextflow Wave integration](https://docs.seqera.io/nextflow/wave) - [Seqera Containers](https://seqera.io/containers/) - Free community container registry diff --git a/platform-enterprise_versioned_docs/version-25.1/getting-started/deployment-options.md b/platform-enterprise_versioned_docs/version-25.1/getting-started/deployment-options.md index 4872023b1..e8d8cb1c3 100644 --- a/platform-enterprise_versioned_docs/version-25.1/getting-started/deployment-options.md +++ b/platform-enterprise_versioned_docs/version-25.1/getting-started/deployment-options.md @@ -86,5 +86,5 @@ If you have an existing environment where you run Nextflow directly, you can sti You can now monitor your workflow runs in the Seqera interface. To configure and execute Nextflow pipelines in cloud environments, see [compute environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-enterprise_versioned_docs/version-25.1/getting-started/proteinfold.mdx b/platform-enterprise_versioned_docs/version-25.1/getting-started/proteinfold.mdx index ffca552af..996165053 100644 --- a/platform-enterprise_versioned_docs/version-25.1/getting-started/proteinfold.mdx +++ b/platform-enterprise_versioned_docs/version-25.1/getting-started/proteinfold.mdx @@ -186,7 +186,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL: `https://github.com/nf-core/proteinfold`. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name: `1.1.1`. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-enterprise_versioned_docs/version-25.1/getting-started/quickstart-demo/launch-pipelines.md b/platform-enterprise_versioned_docs/version-25.1/getting-started/quickstart-demo/launch-pipelines.md index e97fc8702..f530eb6a5 100644 --- a/platform-enterprise_versioned_docs/version-25.1/getting-started/quickstart-demo/launch-pipelines.md +++ b/platform-enterprise_versioned_docs/version-25.1/getting-started/quickstart-demo/launch-pipelines.md @@ -47,7 +47,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- (*Optional*) **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. +- (*Optional*) **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - (*Optional*) **Labels**: Assign new or existing [labels](../../labels/overview) to the run. - **Compute environment**: Select an existing workspace [compute environment](../../compute-envs/overview). diff --git a/platform-enterprise_versioned_docs/version-25.1/getting-started/rnaseq.mdx b/platform-enterprise_versioned_docs/version-25.1/getting-started/rnaseq.mdx index 778c47670..dc0611ffa 100644 --- a/platform-enterprise_versioned_docs/version-25.1/getting-started/rnaseq.mdx +++ b/platform-enterprise_versioned_docs/version-25.1/getting-started/rnaseq.mdx @@ -199,7 +199,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-enterprise_versioned_docs/version-25.1/launch/advanced.md b/platform-enterprise_versioned_docs/version-25.1/launch/advanced.md index 890bd2e5e..4ea569930 100644 --- a/platform-enterprise_versioned_docs/version-25.1/launch/advanced.md +++ b/platform-enterprise_versioned_docs/version-25.1/launch/advanced.md @@ -9,7 +9,7 @@ You can modify the configuration and execution of a pipeline with advanced launc ### Nextflow config file -Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://www.nextflow.io/docs/latest/config.html#config-syntax). +Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax). For example, modify the **manifest** section to give the pipeline a name and description that will show up in the Seqera monitoring section: @@ -106,7 +106,7 @@ Instruct Nextflow to pull the latest pipeline version from the Git repository. T ### Stub run -Replace Nextflow process commands with command [stubs](https://www.nextflow.io/docs/latest/process.html#stub), where defined, before execution. +Replace Nextflow process commands with command [stubs](https://docs.seqera.io/nextflow/process#stub), where defined, before execution. ### Main script diff --git a/platform-enterprise_versioned_docs/version-25.1/launch/cache-resume.mdx b/platform-enterprise_versioned_docs/version-25.1/launch/cache-resume.mdx index 558b0d2ad..ef47bd4d2 100644 --- a/platform-enterprise_versioned_docs/version-25.1/launch/cache-resume.mdx +++ b/platform-enterprise_versioned_docs/version-25.1/launch/cache-resume.mdx @@ -8,13 +8,13 @@ tags: [cache, launch, resume, relaunch] import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; -Nextflow maintains a [cache](https://www.nextflow.io/docs/latest/cache-and-resume.html) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. +Nextflow maintains a [cache](https://docs.seqera.io/nextflow/cache-and-resume) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. ## Cache directory -Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. +Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. -To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://www.nextflow.io/docs/latest/process.html#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). +To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://docs.seqera.io/nextflow/process#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). @@ -108,7 +108,7 @@ Kubernetes compute environments do not use cloud cache by default. To specify a Google Cloud Storage 1. See [these instructions](../compute-envs/google-cloud-batch#iam) to set up IAM and create a JSON key file for the custom service account with permissions to your Google Cloud storage account. - 2. If you run the [gcloud CLI authentication flow](https://nextflow.io/docs/edge/google.html#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. + 2. If you run the [gcloud CLI authentication flow](https://docs.seqera.io/nextflow/google#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. 3. Add the following to the **Nextflow Config file** field when you [launch](../launch/launchpad#launch-form) your pipeline: ```groovy diff --git a/platform-enterprise_versioned_docs/version-25.1/launch/launchpad.md b/platform-enterprise_versioned_docs/version-25.1/launch/launchpad.md index e6636f7ef..4ff9d761e 100644 --- a/platform-enterprise_versioned_docs/version-25.1/launch/launchpad.md +++ b/platform-enterprise_versioned_docs/version-25.1/launch/launchpad.md @@ -35,10 +35,10 @@ For saved pipelines, **General config** and **Run parameters** fields are prefil - **Pipeline to launch**: A Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. Private repositories require [access credentials](../credentials/overview). :::note - Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://www.nextflow.io/docs/latest/sharing.html) in the Nextflow docs for more details. + Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://docs.seqera.io/nextflow/sharing) in the Nextflow docs for more details. ::: - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: A unique identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: The [compute environment](../compute-envs/overview) where the run will be launched. @@ -112,7 +112,7 @@ Use resource labels to tag the computing resources created during the workflow e Secrets are used to store keys and tokens used by workflow tasks to interact with external systems. Enter the names of any stored user or workspace secrets required for the workflow execution. :::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: #### Advanced options diff --git a/platform-enterprise_versioned_docs/version-25.1/monitoring/overview.md b/platform-enterprise_versioned_docs/version-25.1/monitoring/overview.md index 8a35cf2d3..0c04d617d 100644 --- a/platform-enterprise_versioned_docs/version-25.1/monitoring/overview.md +++ b/platform-enterprise_versioned_docs/version-25.1/monitoring/overview.md @@ -12,7 +12,7 @@ The **Runs** tab contains all previous runs in the workspace. Each new or resume - `submitted`: Pending execution - `running`: Running - `succeeded`: Completed successfully -- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://www.nextflow.io/docs/latest/process.html#errorstrategy) +- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://docs.seqera.io/nextflow/process#errorstrategy) - `cancelled`: Stopped manually during execution - `unknown`: Indeterminate status diff --git a/platform-enterprise_versioned_docs/version-25.1/platform-enterprise.md b/platform-enterprise_versioned_docs/version-25.1/platform-enterprise.md index fe4b9c7cd..33a186eca 100644 --- a/platform-enterprise_versioned_docs/version-25.1/platform-enterprise.md +++ b/platform-enterprise_versioned_docs/version-25.1/platform-enterprise.md @@ -28,4 +28,4 @@ Request a [**demo**](https://seqera.io/demo "Seqera Enterprise Demo") to explore Nextflow is both a programming workflow language and an execution runtime that supports a wide range of execution platforms, including popular traditional grid scheduling systems such as Slurm and IBM LSF, and cloud services such as AWS, Azure, and Google Cloud Batch. -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/) to learn more. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/) to learn more. diff --git a/platform-enterprise_versioned_docs/version-25.1/reports/overview.md b/platform-enterprise_versioned_docs/version-25.1/reports/overview.md index c4ba99b1c..59db26855 100644 --- a/platform-enterprise_versioned_docs/version-25.1/reports/overview.md +++ b/platform-enterprise_versioned_docs/version-25.1/reports/overview.md @@ -82,10 +82,10 @@ By default, the MIME type is deduced from the file extension, so you don't need Nextflow can generate a number of built-in reports: -- [Execution report](https://nextflow.io/docs/latest/tracing.html#execution-report) -- [Execution timeline](https://nextflow.io/docs/latest/tracing.html#timeline-report) -- [Trace file](https://nextflow.io/docs/latest/tracing.html#trace-report) -- [Workflow diagram](https://nextflow.io/docs/latest/tracing.html#dag-visualisation) (i.e. DAG) +- [Execution report](https://docs.seqera.io/nextflow/tracing#execution-report) +- [Execution timeline](https://docs.seqera.io/nextflow/tracing#timeline-report) +- [Trace file](https://docs.seqera.io/nextflow/tracing#trace-report) +- [Workflow diagram](https://docs.seqera.io/nextflow/tracing#dag-visualisation) (i.e. DAG) In Nextflow version 24.03.0-edge and later, these reports can be included as pipeline reports in Seqera Platform. Specify them in `tower.yml` like any other file: diff --git a/platform-enterprise_versioned_docs/version-25.1/secrets/overview.md b/platform-enterprise_versioned_docs/version-25.1/secrets/overview.md index e6498a5fd..c5c1d130a 100644 --- a/platform-enterprise_versioned_docs/version-25.1/secrets/overview.md +++ b/platform-enterprise_versioned_docs/version-25.1/secrets/overview.md @@ -31,12 +31,12 @@ Secrets defined by a user have higher priority and will override any secrets wit ## Use secrets in workflows -When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://www.nextflow.io/docs/edge/secrets.html#process-secrets) for more information. +When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://docs.seqera.io/nextflow/secrets) for more information. Secrets are automatically deleted from the secret manager when the pipeline completes, successfully or unsuccessfully. :::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: ## AWS Secrets Manager integration diff --git a/platform-enterprise_versioned_docs/version-25.1/supported_software/dragen/overview.md b/platform-enterprise_versioned_docs/version-25.1/supported_software/dragen/overview.md index 7eaf0d4d4..1bbdb4833 100644 --- a/platform-enterprise_versioned_docs/version-25.1/supported_software/dragen/overview.md +++ b/platform-enterprise_versioned_docs/version-25.1/supported_software/dragen/overview.md @@ -57,7 +57,7 @@ See the [dragen.nf](https://github.com/seqeralabs/nf-dragen/blob/master/modules/ } ``` - See the [Nextflow label docs](https://www.nextflow.io/docs/latest/process.html?highlight=label#label) for more information. + See the [Nextflow label docs](https://docs.seqera.io/nextflow/process.html?highlight=label#label) for more information. 2. Define secrets in Seqera: diff --git a/platform-enterprise_versioned_docs/version-25.1/troubleshooting_and_faqs/azure_troubleshooting.md b/platform-enterprise_versioned_docs/version-25.1/troubleshooting_and_faqs/azure_troubleshooting.md index 9ce13e2e8..3c2430d43 100644 --- a/platform-enterprise_versioned_docs/version-25.1/troubleshooting_and_faqs/azure_troubleshooting.md +++ b/platform-enterprise_versioned_docs/version-25.1/troubleshooting_and_faqs/azure_troubleshooting.md @@ -20,12 +20,12 @@ The default Azure Batch implementation in Seqera Platform uses a single pool for - One [Low priority](https://learn.microsoft.com/en-us/azure/batch/batch-spot-vms#differences-between-spot-and-low-priority-vms) :::note -Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://www.nextflow.io/docs/latest/azure.html#requirements-on-pre-existing-named-pools). +Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://docs.seqera.io/nextflow/azure#requirements-on-pre-existing-named-pools). ::: 2. Create a manual [Azure Batch](../compute-envs/azure-batch#manual) compute environment in Seqera Platform. 3. In **Compute pool name**, specify your dedicated Batch pool. -4. Specify the Low priority pool using the `process.queue` [directive](https://www.nextflow.io/docs/latest/process.html#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. +4. Specify the Low priority pool using the `process.queue` [directive](https://docs.seqera.io/nextflow/process#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. ### Azure Kubernetes Service (AKS) diff --git a/platform-enterprise_versioned_docs/version-25.1/troubleshooting_and_faqs/nextflow.md b/platform-enterprise_versioned_docs/version-25.1/troubleshooting_and_faqs/nextflow.md index fc40fe4a6..168c8b716 100644 --- a/platform-enterprise_versioned_docs/version-25.1/troubleshooting_and_faqs/nextflow.md +++ b/platform-enterprise_versioned_docs/version-25.1/troubleshooting_and_faqs/nextflow.md @@ -19,7 +19,7 @@ To minimize disruption on existing pipelines, version 22.1.x and later are confi **Invoke Nextflow CLI run arguments during Seqera launch** -From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://www.nextflow.io/docs/latest/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): +From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://docs.seqera.io/nextflow/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): ``` export NXF_CLI_OPTS='-dump-hashes' @@ -43,7 +43,7 @@ Currently, you can resolve this by creating empty `main.nf` and `nextflow.config **Use multiple Nextflow configuration files for different environments** -The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) in the main `nextflow.config`. +The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://docs.seqera.io/nextflow/config#config-profiles) in the main `nextflow.config`. Example: @@ -151,7 +151,7 @@ process.afterScript = 'sleep 60' **Jobs remain in RUNNING status when a pipeline run is canceled** -Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: +Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://docs.seqera.io/nextflow/process#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: ``` process terminateError { @@ -195,7 +195,7 @@ The Groovy shell used by Nextflow to execute your workflow has a hard limit on s 1. Remove any unnecessary code or comments from the script. 2. Move long script bodies into a separate script file in the pipeline `/bin` directory. -3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://www.nextflow.io/docs/latest/dsl2.html#modules). +3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://docs.seqera.io/nextflow/dsl2#modules). ### Nextflow Launcher diff --git a/platform-enterprise_versioned_docs/version-25.1/troubleshooting_and_faqs/troubleshooting.md b/platform-enterprise_versioned_docs/version-25.1/troubleshooting_and_faqs/troubleshooting.md index 019f2dc62..b044e6068 100644 --- a/platform-enterprise_versioned_docs/version-25.1/troubleshooting_and_faqs/troubleshooting.md +++ b/platform-enterprise_versioned_docs/version-25.1/troubleshooting_and_faqs/troubleshooting.md @@ -47,7 +47,7 @@ This error can occur if you execute a DSL1-based Nextflow workflow using [Nextfl The `sleep` commands in your Nextflow workflows may differ in behavior depending on where they are: - If used within an `errorStrategy` block, the Groovy sleep function will be used (which takes its value in milliseconds). -- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://www.nextflow.io/docs/latest/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. +- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://docs.seqera.io/nextflow/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. **Large number of batch job definitions** diff --git a/platform-enterprise_versioned_docs/version-25.2/compute-envs/aws-batch.md b/platform-enterprise_versioned_docs/version-25.2/compute-envs/aws-batch.md index f0e207873..a0e93594e 100644 --- a/platform-enterprise_versioned_docs/version-25.2/compute-envs/aws-batch.md +++ b/platform-enterprise_versioned_docs/version-25.2/compute-envs/aws-batch.md @@ -686,7 +686,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM 1. In the **Pipeline work directory** field type or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation), e.g., `s3://seqera-bucket`. The work directory can be customized to specify a folder inside the bucket where Nextflow intermediate files will be stored, e.g., `s3://seqera-bucket/nextflow-workdir`. The bucket must be located in the same region chosen in the previous step. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -695,7 +695,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM Using an EFS or FSx file system as your work directory is currently incompatible with [Studios](../studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
@@ -918,7 +918,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See 1. Select a **Region**, e.g., _eu-west-1 - Europe (Ireland)_. This region must match the region where your S3 bucket or EFS/FSx work directory is located to avoid high data transfer costs. 1. Enter or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation) in the **Pipeline work directory** field, e.g., `s3://seqera-bucket`. This bucket must be in the same region chosen in the previous step to avoid incurring high data transfer costs. The work directory can be customized to specify a folder inside the bucket, e.g., `s3://seqera-bucket/nextflow-workdir`. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -927,7 +927,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See Using an EFS or FSx file system as your work directory is currently incompatible with [Studios](../studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
diff --git a/platform-enterprise_versioned_docs/version-25.2/compute-envs/azure-batch.md b/platform-enterprise_versioned_docs/version-25.2/compute-envs/azure-batch.md index 984285403..d9ffcb595 100644 --- a/platform-enterprise_versioned_docs/version-25.2/compute-envs/azure-batch.md +++ b/platform-enterprise_versioned_docs/version-25.2/compute-envs/azure-batch.md @@ -190,7 +190,7 @@ Nextflow can authenticate to Azure services using a managed identity. This metho When you use a manually-configured compute environment with a managed identity attached to the Azure Batch Pool, Nextflow can use this managed identity for authentication. However, Seqera still needs to use access keys or an Entra service principal to submit the initial task to Azure Batch to run Nextflow, which will then proceed with the managed identity for subsequent authentication. 1. In Azure, create a user-assigned managed identity. See [Manage user-assigned managed identities](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-manage-user-assigned-managed-identities) for detailed steps. Take note of the client ID of the managed identity when you create it. -1. The user-assigned managed identity must have the necessary access roles for Nextflow. See [Required role assignments](https://www.nextflow.io/docs/latest/azure.html#required-role-assignments) for more information. +1. The user-assigned managed identity must have the necessary access roles for Nextflow. See [Required role assignments](https://docs.seqera.io/nextflow/azure#required-role-assignments) for more information. 1. Associate the user-assigned managed identity with the Azure Batch Pool. See [Set up managed identity in your Batch pool](https://learn.microsoft.com/en-us/troubleshoot/azure/hpc/batch/use-managed-identities-azure-batch-account-pool#set-up-managed-identity-in-your-batch-pool) for more information. 1. When you set up the Seqera compute environment, select the Azure Batch pool by name and enter the managed identity client ID in the specified field as instructed above. @@ -253,7 +253,7 @@ Create a Batch Forge Azure Batch compute environment: 1. Select a **Region**, such as _eastus_. 1. In the **Pipeline work directory** field, enter the Azure blob container created previously. For example, `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. 1. Select **Enable Fusion v2** to allow access to your Azure Blob Storage data via the [Fusion v2][fusion-docs] virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. @@ -286,7 +286,7 @@ Create a Batch Forge Azure Batch compute environment: 1. Enter the **VMs count**. If autoscaling is enabled (default), this is the maximum number of VMs you wish the pool to scale up to. If autoscaling is disabled, this is the fixed number of virtual machines in the pool. 1. Enable **Autoscale** to scale up and down automatically, based on the number of pipeline tasks. The number of VMs will vary from **0** to **VMs count**. 1. Enable **Dispose resources** for Seqera to automatically delete the Batch pool if the compute environment is deleted on the platform. -1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://www.nextflow.io/docs/latest/wave.html) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. +1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://docs.seqera.io/nextflow/wave) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. 1. Apply [**Resource labels**](../resource-labels/overview). This will populate the **Metadata** fields of the Azure Batch pool. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. @@ -397,7 +397,7 @@ The following settings can be modified after creating a pool: 1. Select a **Region**, such as _eastus (East US)_. 1. In the **Pipeline work directory** field, add the Azure blob container created previously. For example, `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. 1. Select **Enable Fusion v2** to allow access to your Azure Blob Storage data via the [Fusion v2][fusion-docs] virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. @@ -464,7 +464,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [az-vm-gen]: https://learn.microsoft.com/en-us/azure/virtual-machines/generation-2 [az-disk-type]: https://learn.microsoft.com/en-us/azure/virtual-machines/disks-types [az-batch-autoscale]: https://learn.microsoft.com/en-us/azure/batch/batch-automatic-scaling -[az-file-shares]: https://www.nextflow.io/docs/latest/azure.html#azure-file-shares +[az-file-shares]: https://docs.seqera.io/nextflow/azure#azure-file-shares [az-vm-sizes]: https://learn.microsoft.com/en-us/azure/virtual-machines/sizes/overview [wave-docs]: https://docs.seqera.io/wave diff --git a/platform-enterprise_versioned_docs/version-25.2/compute-envs/google-cloud-batch.md b/platform-enterprise_versioned_docs/version-25.2/compute-envs/google-cloud-batch.md index d277a835e..4fd7c8c49 100644 --- a/platform-enterprise_versioned_docs/version-25.2/compute-envs/google-cloud-batch.md +++ b/platform-enterprise_versioned_docs/version-25.2/compute-envs/google-cloud-batch.md @@ -147,7 +147,7 @@ Select the **Location** where you will execute your pipelines. See [Location][lo In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the location selected in the previous step. :::note -When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. +When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: #### Seqera features @@ -171,7 +171,7 @@ Select **Enable Fusion v2** to allow access to your Google Cloud Storage data vi :::note To specify virtual machine settings in Platform during compute environment creation, use the **Global Nextflow config** field to apply custom Nextflow process directives to all pipeline runs launched with this compute environment. - To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://www.nextflow.io/docs/latest/google.html#process-definition) for more information. + To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://docs.seqera.io/nextflow/google#process-definition) for more information. ::: When Fusion v2 is enabled, the following virtual machine settings are applied: @@ -231,7 +231,7 @@ If you use VM instance templates for the head or compute jobs (see step 6 below) :::caution Seqera does not validate the VM instance template you specify in these fields. Generally, use templates that define only the machine type, network, disk, and configuration values that will not change across multiple VM instances and Seqera compute environments. See [Create instance templates](https://cloud.google.com/compute/docs/instance-templates/create-instance-templates) for instructions to create your instance templates. - To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://www.nextflow.io/docs/latest/google.html#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://www.nextflow.io/docs/latest/config.html#config-process-selectors) to assign separate templates to each of your processes. + To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://docs.seqera.io/nextflow/google#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://docs.seqera.io/nextflow/config#config-process-selectors) to assign separate templates to each of your processes. ::: Select **Create** to finalize the compute environment setup. @@ -244,7 +244,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [create-sa]: https://cloud.google.com/iam/docs/service-accounts-create#creating [get-json]: https://cloud.google.com/iam/docs/keys-list-get#get-key [location]: https://cloud.google.com/compute/docs/regions-zones#available -[wave-docs]: https://www.nextflow.io/docs/latest/wave.html +[wave-docs]: https://docs.seqera.io/nextflow/wave [fusion-docs]: https://docs.seqera.io/fusion [platform-fusion-docs]: ../supported_software/fusion/overview [pre-post-run-scripts]: ../launch/advanced#pre-and-post-run-scripts diff --git a/platform-enterprise_versioned_docs/version-25.2/compute-envs/hpc.md b/platform-enterprise_versioned_docs/version-25.2/compute-envs/hpc.md index 3c18037a1..98cd817b8 100644 --- a/platform-enterprise_versioned_docs/version-25.2/compute-envs/hpc.md +++ b/platform-enterprise_versioned_docs/version-25.2/compute-envs/hpc.md @@ -64,8 +64,8 @@ To create a new **HPC** compute environment: 1. Enter the absolute path of the **Launch directory** to be used on the cluster. If omitted, it will be the same as the work directory. 1. Enter the **Login hostname**. This is usually the hostname or public IP address of the cluster's login node. -1. Enter the **Head queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will be submitted. -1. Enter the **Compute queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will submit tasks. +1. Enter the **Head queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will be submitted. +1. Enter the **Compute queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will submit tasks. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. diff --git a/platform-enterprise_versioned_docs/version-25.2/compute-envs/overview.md b/platform-enterprise_versioned_docs/version-25.2/compute-envs/overview.md index b888a301c..4d3a1d6cb 100644 --- a/platform-enterprise_versioned_docs/version-25.2/compute-envs/overview.md +++ b/platform-enterprise_versioned_docs/version-25.2/compute-envs/overview.md @@ -49,8 +49,8 @@ Some important considerations: - Seqera only supports NVIDIA GPUs. Select instances with NVIDIA GPUs for your GPU-dependent processes. - The **Enable GPUs** setting causes Batch Forge to specify the most current [AWS-recommended GPU-optimized ECS AMI](https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ecs-optimized_AMI.html) as the EC2 fleet AMI when creating the compute environment. This setting can be overridden by **AMI ID** in the advanced options. - The **Enable GPUs** setting alone does not deploy GPU instances in your compute environment. You must still specify GPU-enabled instance types in the **Advanced options > Instance types** field. -- Your Nextflow script must include [accelerator directives](https://www.nextflow.io/docs/latest/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. -- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: +- Your Nextflow script must include [accelerator directives](https://docs.seqera.io/nextflow/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. +- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://docs.seqera.io/nextflow/process#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: ```groovy process { diff --git a/platform-enterprise_versioned_docs/version-25.2/enterprise/advanced-topics/manual-azure-batch-setup.md b/platform-enterprise_versioned_docs/version-25.2/enterprise/advanced-topics/manual-azure-batch-setup.md index 4e7c9894d..473311c80 100644 --- a/platform-enterprise_versioned_docs/version-25.2/enterprise/advanced-topics/manual-azure-batch-setup.md +++ b/platform-enterprise_versioned_docs/version-25.2/enterprise/advanced-topics/manual-azure-batch-setup.md @@ -320,7 +320,7 @@ Select **Launch** next to the `hello-world-autopool-low-priority` pipeline in yo Seqera can utilize an Azure Entra service principal to authenticate and access Azure Batch for job execution and Azure Storage for data management, and Nextflow can authenticate to Azure services using a managed identity. This method offers enhanced security compared to access keys, but must run on Azure infrastructure. -See [Microsoft Entra](https://www.nextflow.io/docs/latest/azure.html#microsoft-entra) in the Nextflow documentation for more information. +See [Microsoft Entra](https://docs.seqera.io/nextflow/azure#microsoft-entra) in the Nextflow documentation for more information. #### Create a service principal for Seqera to use for authentication @@ -340,7 +340,7 @@ In Seqera: Back in the Azure Portal: 1. [Create a managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-manage-user-assigned-managed-identities?pivots=identity-mi-methods-azp) -1. [Assign the relevant roles to the managed identity](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current). See [Required role assignments](https://www.nextflow.io/docs/latest/azure.html#required-role-assignments) for Nextflow requirements. +1. [Assign the relevant roles to the managed identity](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current). See [Required role assignments](https://docs.seqera.io/nextflow/azure#required-role-assignments) for Nextflow requirements. 1. Note the managed identity client ID for later. 1. In the Azure Portal, go to the Batch account you created earlier. 1. Go to the **Pools** tab and find the pool called `tower-pool-${id}`, where `${id}` is the ID of the head node pool created earlier. @@ -481,6 +481,6 @@ If you wish to keep the Azure resources, you can remove each pool within a Batch [install-azure-cli]: https://learn.microsoft.com/en-us/cli/azure/install-azure-cli [install-seqera-cli]: /platform-cli/installation -[nextflow-working-directory]: https://www.nextflow.io/docs/latest/cache-and-resume.html#work-directory +[nextflow-working-directory]: https://docs.seqera.io/nextflow/cache-and-resume#work-directory [create-org-workspace]: ../../getting-started/workspace-setup [add-pipeline]: ../../getting-started/quickstart-demo/add-pipelines#add-from-the-launchpad diff --git a/platform-enterprise_versioned_docs/version-25.2/enterprise/configuration/wave.md b/platform-enterprise_versioned_docs/version-25.2/enterprise/configuration/wave.md index b84fe0534..8d84565f1 100644 --- a/platform-enterprise_versioned_docs/version-25.2/enterprise/configuration/wave.md +++ b/platform-enterprise_versioned_docs/version-25.2/enterprise/configuration/wave.md @@ -79,5 +79,5 @@ See the [Wave documentation](https://docs.seqera.io/wave) for installation and c ## Additional resources - [Wave documentation](https://docs.seqera.io/wave) -- [Nextflow Wave integration](https://www.nextflow.io/docs/latest/wave.html) +- [Nextflow Wave integration](https://docs.seqera.io/nextflow/wave) - [Seqera Containers](https://seqera.io/containers/) - Free community container registry diff --git a/platform-enterprise_versioned_docs/version-25.2/getting-started/deployment-options.md b/platform-enterprise_versioned_docs/version-25.2/getting-started/deployment-options.md index 7fe24fd1a..49e4f2f87 100644 --- a/platform-enterprise_versioned_docs/version-25.2/getting-started/deployment-options.md +++ b/platform-enterprise_versioned_docs/version-25.2/getting-started/deployment-options.md @@ -86,5 +86,5 @@ If you have an existing environment where you run Nextflow directly, you can sti You can now monitor your workflow runs in the Seqera interface. To configure and execute Nextflow pipelines in cloud environments, see [compute environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-enterprise_versioned_docs/version-25.2/getting-started/proteinfold.md b/platform-enterprise_versioned_docs/version-25.2/getting-started/proteinfold.md index c3f52ced6..385bcbb14 100644 --- a/platform-enterprise_versioned_docs/version-25.2/getting-started/proteinfold.md +++ b/platform-enterprise_versioned_docs/version-25.2/getting-started/proteinfold.md @@ -185,7 +185,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL: `https://github.com/nf-core/proteinfold`. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name: `1.1.1`. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-enterprise_versioned_docs/version-25.2/getting-started/quickstart-demo/launch-pipelines.md b/platform-enterprise_versioned_docs/version-25.2/getting-started/quickstart-demo/launch-pipelines.md index 6c9d6309b..f63269fdc 100644 --- a/platform-enterprise_versioned_docs/version-25.2/getting-started/quickstart-demo/launch-pipelines.md +++ b/platform-enterprise_versioned_docs/version-25.2/getting-started/quickstart-demo/launch-pipelines.md @@ -47,7 +47,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- (*Optional*) **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. +- (*Optional*) **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - (*Optional*) **Labels**: Assign new or existing [labels](../../labels/overview) to the run. - **Compute environment**: Select an existing workspace [compute environment](../../compute-envs/overview). diff --git a/platform-enterprise_versioned_docs/version-25.2/getting-started/rnaseq.md b/platform-enterprise_versioned_docs/version-25.2/getting-started/rnaseq.md index b08c961b0..60ef78419 100644 --- a/platform-enterprise_versioned_docs/version-25.2/getting-started/rnaseq.md +++ b/platform-enterprise_versioned_docs/version-25.2/getting-started/rnaseq.md @@ -196,7 +196,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-enterprise_versioned_docs/version-25.2/launch/advanced.md b/platform-enterprise_versioned_docs/version-25.2/launch/advanced.md index ca982b695..62140d486 100644 --- a/platform-enterprise_versioned_docs/version-25.2/launch/advanced.md +++ b/platform-enterprise_versioned_docs/version-25.2/launch/advanced.md @@ -10,7 +10,7 @@ You can modify the configuration and execution of a pipeline with advanced launc ### Nextflow config file -Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://www.nextflow.io/docs/latest/config.html#config-syntax). +Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax). For example, modify the **manifest** section to give the pipeline a name and description that will show up in the Seqera monitoring section: @@ -107,7 +107,7 @@ Instruct Nextflow to pull the latest pipeline version from the Git repository. T ### Stub run -Replace Nextflow process commands with command [stubs](https://www.nextflow.io/docs/latest/process.html#stub), where defined, before execution. +Replace Nextflow process commands with command [stubs](https://docs.seqera.io/nextflow/process#stub), where defined, before execution. ### Main script diff --git a/platform-enterprise_versioned_docs/version-25.2/launch/cache-resume.mdx b/platform-enterprise_versioned_docs/version-25.2/launch/cache-resume.mdx index 22b22fab7..35c73740d 100644 --- a/platform-enterprise_versioned_docs/version-25.2/launch/cache-resume.mdx +++ b/platform-enterprise_versioned_docs/version-25.2/launch/cache-resume.mdx @@ -9,13 +9,13 @@ tags: [cache, launch, resume, relaunch] import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; -Nextflow maintains a [cache](https://www.nextflow.io/docs/latest/cache-and-resume.html) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. +Nextflow maintains a [cache](https://docs.seqera.io/nextflow/cache-and-resume) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. ## Cache directory -Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. +Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. -To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://www.nextflow.io/docs/latest/process.html#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). +To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://docs.seqera.io/nextflow/process#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). @@ -109,7 +109,7 @@ Kubernetes compute environments do not use cloud cache by default. To specify a Google Cloud Storage 1. See [these instructions](../compute-envs/google-cloud-batch#iam) to set up IAM and create a JSON key file for the custom service account with permissions to your Google Cloud storage account. - 2. If you run the [gcloud CLI authentication flow](https://nextflow.io/docs/edge/google.html#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. + 2. If you run the [gcloud CLI authentication flow](https://docs.seqera.io/nextflow/google#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. 3. Add the following to the **Nextflow Config file** field when you [launch](../launch/launchpad#launch-form) your pipeline: ```groovy diff --git a/platform-enterprise_versioned_docs/version-25.2/launch/launchpad.md b/platform-enterprise_versioned_docs/version-25.2/launch/launchpad.md index 5e2f1ea93..449b81b90 100644 --- a/platform-enterprise_versioned_docs/version-25.2/launch/launchpad.md +++ b/platform-enterprise_versioned_docs/version-25.2/launch/launchpad.md @@ -37,10 +37,10 @@ The launch form accepts URL query parameters. See [Populate launch form with URL - **Pipeline to launch**: A Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. Private repositories require [access credentials](../credentials/overview). :::note - Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://www.nextflow.io/docs/latest/sharing.html) in the Nextflow docs for more details. + Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://docs.seqera.io/nextflow/sharing) in the Nextflow docs for more details. ::: - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: A unique identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: The [compute environment](../compute-envs/overview) where the run will be launched. @@ -115,7 +115,7 @@ Use resource labels to tag the computing resources created during the workflow e Secrets are used to store keys and tokens used by workflow tasks to interact with external systems. Enter the names of any stored user or workspace secrets required for the workflow execution. :::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: #### Advanced options diff --git a/platform-enterprise_versioned_docs/version-25.2/monitoring/overview.md b/platform-enterprise_versioned_docs/version-25.2/monitoring/overview.md index 53b40928e..6a9e1b66e 100644 --- a/platform-enterprise_versioned_docs/version-25.2/monitoring/overview.md +++ b/platform-enterprise_versioned_docs/version-25.2/monitoring/overview.md @@ -13,7 +13,7 @@ The **Runs** tab contains all previous runs in the workspace. Each new or resume - `submitted`: Pending execution - `running`: Running - `succeeded`: Completed successfully -- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://www.nextflow.io/docs/latest/process.html#errorstrategy) +- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://docs.seqera.io/nextflow/process#errorstrategy) - `cancelled`: Stopped manually during execution - `unknown`: Indeterminate status diff --git a/platform-enterprise_versioned_docs/version-25.2/platform-enterprise.md b/platform-enterprise_versioned_docs/version-25.2/platform-enterprise.md index e32595db8..bc837db8f 100644 --- a/platform-enterprise_versioned_docs/version-25.2/platform-enterprise.md +++ b/platform-enterprise_versioned_docs/version-25.2/platform-enterprise.md @@ -29,4 +29,4 @@ Request a [**demo**](https://seqera.io/demo "Seqera Enterprise Demo") to explore Nextflow is both a programming workflow language and an execution runtime that supports a wide range of execution platforms, including popular traditional grid scheduling systems such as Slurm and IBM LSF, and cloud services such as AWS, Azure, and Google Cloud Batch. -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/) to learn more. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/) to learn more. diff --git a/platform-enterprise_versioned_docs/version-25.2/reports/overview.md b/platform-enterprise_versioned_docs/version-25.2/reports/overview.md index c4ba99b1c..59db26855 100644 --- a/platform-enterprise_versioned_docs/version-25.2/reports/overview.md +++ b/platform-enterprise_versioned_docs/version-25.2/reports/overview.md @@ -82,10 +82,10 @@ By default, the MIME type is deduced from the file extension, so you don't need Nextflow can generate a number of built-in reports: -- [Execution report](https://nextflow.io/docs/latest/tracing.html#execution-report) -- [Execution timeline](https://nextflow.io/docs/latest/tracing.html#timeline-report) -- [Trace file](https://nextflow.io/docs/latest/tracing.html#trace-report) -- [Workflow diagram](https://nextflow.io/docs/latest/tracing.html#dag-visualisation) (i.e. DAG) +- [Execution report](https://docs.seqera.io/nextflow/tracing#execution-report) +- [Execution timeline](https://docs.seqera.io/nextflow/tracing#timeline-report) +- [Trace file](https://docs.seqera.io/nextflow/tracing#trace-report) +- [Workflow diagram](https://docs.seqera.io/nextflow/tracing#dag-visualisation) (i.e. DAG) In Nextflow version 24.03.0-edge and later, these reports can be included as pipeline reports in Seqera Platform. Specify them in `tower.yml` like any other file: diff --git a/platform-enterprise_versioned_docs/version-25.2/secrets/overview.md b/platform-enterprise_versioned_docs/version-25.2/secrets/overview.md index e6498a5fd..c5c1d130a 100644 --- a/platform-enterprise_versioned_docs/version-25.2/secrets/overview.md +++ b/platform-enterprise_versioned_docs/version-25.2/secrets/overview.md @@ -31,12 +31,12 @@ Secrets defined by a user have higher priority and will override any secrets wit ## Use secrets in workflows -When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://www.nextflow.io/docs/edge/secrets.html#process-secrets) for more information. +When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://docs.seqera.io/nextflow/secrets) for more information. Secrets are automatically deleted from the secret manager when the pipeline completes, successfully or unsuccessfully. :::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: ## AWS Secrets Manager integration diff --git a/platform-enterprise_versioned_docs/version-25.2/supported_software/dragen/overview.md b/platform-enterprise_versioned_docs/version-25.2/supported_software/dragen/overview.md index 90b17c409..0ab3e9023 100644 --- a/platform-enterprise_versioned_docs/version-25.2/supported_software/dragen/overview.md +++ b/platform-enterprise_versioned_docs/version-25.2/supported_software/dragen/overview.md @@ -80,7 +80,7 @@ See the [dragen.nf](https://github.com/seqeralabs/nf-dragen/blob/master/modules/ } ``` - See the [Nextflow label docs](https://www.nextflow.io/docs/latest/process.html?highlight=label#label) for more information. + See the [Nextflow label docs](https://docs.seqera.io/nextflow/process.html?highlight=label#label) for more information. 2. Define secrets in Seqera: diff --git a/platform-enterprise_versioned_docs/version-25.2/troubleshooting_and_faqs/azure_troubleshooting.md b/platform-enterprise_versioned_docs/version-25.2/troubleshooting_and_faqs/azure_troubleshooting.md index 29bd4d91d..9e63abdaa 100644 --- a/platform-enterprise_versioned_docs/version-25.2/troubleshooting_and_faqs/azure_troubleshooting.md +++ b/platform-enterprise_versioned_docs/version-25.2/troubleshooting_and_faqs/azure_troubleshooting.md @@ -16,12 +16,12 @@ The default Azure Batch implementation in Seqera Platform uses a single pool for - One [Low priority](https://learn.microsoft.com/en-us/azure/batch/batch-spot-vms#differences-between-spot-and-low-priority-vms) :::note -Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://www.nextflow.io/docs/latest/azure.html#requirements-on-pre-existing-named-pools). +Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://docs.seqera.io/nextflow/azure#requirements-on-pre-existing-named-pools). ::: 2. Create a manual [Azure Batch](../compute-envs/azure-batch#manual) compute environment in Seqera Platform. 3. In **Compute pool name**, specify your dedicated Batch pool. -4. Specify the Low priority pool using the `process.queue` [directive](https://www.nextflow.io/docs/latest/process.html#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. +4. Specify the Low priority pool using the `process.queue` [directive](https://docs.seqera.io/nextflow/process#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. ### Azure Kubernetes Service (AKS) diff --git a/platform-enterprise_versioned_docs/version-25.2/troubleshooting_and_faqs/nextflow.md b/platform-enterprise_versioned_docs/version-25.2/troubleshooting_and_faqs/nextflow.md index e8003814e..89d0feeba 100644 --- a/platform-enterprise_versioned_docs/version-25.2/troubleshooting_and_faqs/nextflow.md +++ b/platform-enterprise_versioned_docs/version-25.2/troubleshooting_and_faqs/nextflow.md @@ -20,7 +20,7 @@ To minimize disruption on existing pipelines, version 22.1.x and later are confi **Invoke Nextflow CLI run arguments during Seqera launch** -From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://www.nextflow.io/docs/latest/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): +From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://docs.seqera.io/nextflow/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): ``` export NXF_CLI_OPTS='-dump-hashes' @@ -44,7 +44,7 @@ Currently, you can resolve this by creating empty `main.nf` and `nextflow.config **Use multiple Nextflow configuration files for different environments** -The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) in the main `nextflow.config`. +The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://docs.seqera.io/nextflow/config#config-profiles) in the main `nextflow.config`. Example: @@ -152,7 +152,7 @@ process.afterScript = 'sleep 60' **Jobs remain in RUNNING status when a pipeline run is canceled** -Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: +Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://docs.seqera.io/nextflow/process#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: ``` process terminateError { @@ -196,7 +196,7 @@ The Groovy shell used by Nextflow to execute your workflow has a hard limit on s 1. Remove any unnecessary code or comments from the script. 2. Move long script bodies into a separate script file in the pipeline `/bin` directory. -3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://www.nextflow.io/docs/latest/dsl2.html#modules). +3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://docs.seqera.io/nextflow/dsl2#modules). ### Nextflow Launcher diff --git a/platform-enterprise_versioned_docs/version-25.2/troubleshooting_and_faqs/troubleshooting.md b/platform-enterprise_versioned_docs/version-25.2/troubleshooting_and_faqs/troubleshooting.md index 019f2dc62..b044e6068 100644 --- a/platform-enterprise_versioned_docs/version-25.2/troubleshooting_and_faqs/troubleshooting.md +++ b/platform-enterprise_versioned_docs/version-25.2/troubleshooting_and_faqs/troubleshooting.md @@ -47,7 +47,7 @@ This error can occur if you execute a DSL1-based Nextflow workflow using [Nextfl The `sleep` commands in your Nextflow workflows may differ in behavior depending on where they are: - If used within an `errorStrategy` block, the Groovy sleep function will be used (which takes its value in milliseconds). -- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://www.nextflow.io/docs/latest/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. +- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://docs.seqera.io/nextflow/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. **Large number of batch job definitions** diff --git a/platform-enterprise_versioned_docs/version-25.3/compute-envs/aws-batch.md b/platform-enterprise_versioned_docs/version-25.3/compute-envs/aws-batch.md index f0e207873..a0e93594e 100644 --- a/platform-enterprise_versioned_docs/version-25.3/compute-envs/aws-batch.md +++ b/platform-enterprise_versioned_docs/version-25.3/compute-envs/aws-batch.md @@ -686,7 +686,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM 1. In the **Pipeline work directory** field type or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation), e.g., `s3://seqera-bucket`. The work directory can be customized to specify a folder inside the bucket where Nextflow intermediate files will be stored, e.g., `s3://seqera-bucket/nextflow-workdir`. The bucket must be located in the same region chosen in the previous step. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -695,7 +695,7 @@ Depending on the provided configuration in the UI, Seqera might also create IAM Using an EFS or FSx file system as your work directory is currently incompatible with [Studios](../studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
@@ -918,7 +918,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See 1. Select a **Region**, e.g., _eu-west-1 - Europe (Ireland)_. This region must match the region where your S3 bucket or EFS/FSx work directory is located to avoid high data transfer costs. 1. Enter or select from the dropdown menu the S3 bucket [previously created](#s3-bucket-creation) in the **Pipeline work directory** field, e.g., `s3://seqera-bucket`. This bucket must be in the same region chosen in the previous step to avoid incurring high data transfer costs. The work directory can be customized to specify a folder inside the bucket, e.g., `s3://seqera-bucket/nextflow-workdir`. :::note - When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify an S3 bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. Seqera adds a `cloudcache` block to the Nextflow configuration file for all runs executed with this compute environment. This block includes the path to a `cloudcache` folder in your work directory, e.g., `s3://seqera-bucket/cloudcache/.cache`. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: Similarly you can specify a path in an EFS or FSx file system as your work directory. When using EFS or FSx, you'll need to scroll down to "EFS file system" or "FSx for Lustre" sections to specify either an existing file system ID or let Seqera create a new one for you automatically. Read the notes in steps 23 and 24 below on how to setup EFS or FSx. @@ -927,7 +927,7 @@ AWS Batch creates resources that you may be charged for in your AWS account. See Using an EFS or FSx file system as your work directory is currently incompatible with [Studios](../studios/overview), and will result in errors with checkpoints and mounted data. Use an S3 bucket as your work directory when using Studios. ::: -1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://www.nextflow.io/docs/latest/wave.html) for more information. +1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers](https://docs.seqera.io/nextflow/wave) for more information. 1. Select **Enable Fusion v2** to allow access to your S3-hosted data via the [Fusion v2](https://docs.seqera.io/fusion) virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details.
diff --git a/platform-enterprise_versioned_docs/version-25.3/compute-envs/azure-batch.md b/platform-enterprise_versioned_docs/version-25.3/compute-envs/azure-batch.md index 984285403..d9ffcb595 100644 --- a/platform-enterprise_versioned_docs/version-25.3/compute-envs/azure-batch.md +++ b/platform-enterprise_versioned_docs/version-25.3/compute-envs/azure-batch.md @@ -190,7 +190,7 @@ Nextflow can authenticate to Azure services using a managed identity. This metho When you use a manually-configured compute environment with a managed identity attached to the Azure Batch Pool, Nextflow can use this managed identity for authentication. However, Seqera still needs to use access keys or an Entra service principal to submit the initial task to Azure Batch to run Nextflow, which will then proceed with the managed identity for subsequent authentication. 1. In Azure, create a user-assigned managed identity. See [Manage user-assigned managed identities](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-manage-user-assigned-managed-identities) for detailed steps. Take note of the client ID of the managed identity when you create it. -1. The user-assigned managed identity must have the necessary access roles for Nextflow. See [Required role assignments](https://www.nextflow.io/docs/latest/azure.html#required-role-assignments) for more information. +1. The user-assigned managed identity must have the necessary access roles for Nextflow. See [Required role assignments](https://docs.seqera.io/nextflow/azure#required-role-assignments) for more information. 1. Associate the user-assigned managed identity with the Azure Batch Pool. See [Set up managed identity in your Batch pool](https://learn.microsoft.com/en-us/troubleshoot/azure/hpc/batch/use-managed-identities-azure-batch-account-pool#set-up-managed-identity-in-your-batch-pool) for more information. 1. When you set up the Seqera compute environment, select the Azure Batch pool by name and enter the managed identity client ID in the specified field as instructed above. @@ -253,7 +253,7 @@ Create a Batch Forge Azure Batch compute environment: 1. Select a **Region**, such as _eastus_. 1. In the **Pipeline work directory** field, enter the Azure blob container created previously. For example, `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. 1. Select **Enable Fusion v2** to allow access to your Azure Blob Storage data via the [Fusion v2][fusion-docs] virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. @@ -286,7 +286,7 @@ Create a Batch Forge Azure Batch compute environment: 1. Enter the **VMs count**. If autoscaling is enabled (default), this is the maximum number of VMs you wish the pool to scale up to. If autoscaling is disabled, this is the fixed number of virtual machines in the pool. 1. Enable **Autoscale** to scale up and down automatically, based on the number of pipeline tasks. The number of VMs will vary from **0** to **VMs count**. 1. Enable **Dispose resources** for Seqera to automatically delete the Batch pool if the compute environment is deleted on the platform. -1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://www.nextflow.io/docs/latest/wave.html) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. +1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials) to authenticate a registry (used by the [Wave containers](https://docs.seqera.io/nextflow/wave) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance. 1. Apply [**Resource labels**](../resource-labels/overview). This will populate the **Metadata** fields of the Azure Batch pool. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. @@ -397,7 +397,7 @@ The following settings can be modified after creating a pool: 1. Select a **Region**, such as _eastus (East US)_. 1. In the **Pipeline work directory** field, add the Azure blob container created previously. For example, `az://seqeracomputestorage-container/work`. :::note - When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. + When you specify a Blob Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: 1. Select **Enable Wave containers** to facilitate access to private container repositories and provision containers in your pipelines using the Wave containers service. See [Wave containers][wave-docs] for more information. 1. Select **Enable Fusion v2** to allow access to your Azure Blob Storage data via the [Fusion v2][fusion-docs] virtual distributed file system. This speeds up most data operations. The Fusion v2 file system requires Wave containers to be enabled. See [Fusion file system](../supported_software/fusion/overview) for configuration details. @@ -464,7 +464,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [az-vm-gen]: https://learn.microsoft.com/en-us/azure/virtual-machines/generation-2 [az-disk-type]: https://learn.microsoft.com/en-us/azure/virtual-machines/disks-types [az-batch-autoscale]: https://learn.microsoft.com/en-us/azure/batch/batch-automatic-scaling -[az-file-shares]: https://www.nextflow.io/docs/latest/azure.html#azure-file-shares +[az-file-shares]: https://docs.seqera.io/nextflow/azure#azure-file-shares [az-vm-sizes]: https://learn.microsoft.com/en-us/azure/virtual-machines/sizes/overview [wave-docs]: https://docs.seqera.io/wave diff --git a/platform-enterprise_versioned_docs/version-25.3/compute-envs/google-cloud-batch.md b/platform-enterprise_versioned_docs/version-25.3/compute-envs/google-cloud-batch.md index d277a835e..4fd7c8c49 100644 --- a/platform-enterprise_versioned_docs/version-25.3/compute-envs/google-cloud-batch.md +++ b/platform-enterprise_versioned_docs/version-25.3/compute-envs/google-cloud-batch.md @@ -147,7 +147,7 @@ Select the **Location** where you will execute your pipelines. See [Location][lo In the **Pipeline work directory** field, enter your storage bucket URL, e.g., `gs://my-bucket`. This bucket must be accessible in the location selected in the previous step. :::note -When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. +When you specify a Cloud Storage bucket as your work directory, this bucket is used for the Nextflow [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) by default. You can specify an alternative cache location with the **Nextflow config file** field on the pipeline [launch](../launch/launchpad#launch-form) form. ::: #### Seqera features @@ -171,7 +171,7 @@ Select **Enable Fusion v2** to allow access to your Google Cloud Storage data vi :::note To specify virtual machine settings in Platform during compute environment creation, use the **Global Nextflow config** field to apply custom Nextflow process directives to all pipeline runs launched with this compute environment. - To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://www.nextflow.io/docs/latest/google.html#process-definition) for more information. + To specify virtual machine settings per pipeline run in Platform, or as a persistent configuration in your Nextflow pipeline repository, use Nextflow process directives. See [Google Cloud Batch process definition](https://docs.seqera.io/nextflow/google#process-definition) for more information. ::: When Fusion v2 is enabled, the following virtual machine settings are applied: @@ -231,7 +231,7 @@ If you use VM instance templates for the head or compute jobs (see step 6 below) :::caution Seqera does not validate the VM instance template you specify in these fields. Generally, use templates that define only the machine type, network, disk, and configuration values that will not change across multiple VM instances and Seqera compute environments. See [Create instance templates](https://cloud.google.com/compute/docs/instance-templates/create-instance-templates) for instructions to create your instance templates. - To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://www.nextflow.io/docs/latest/google.html#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://www.nextflow.io/docs/latest/config.html#config-process-selectors) to assign separate templates to each of your processes. + To prevent errors during workflow execution, ensure that the instance templates you use are suitably configured for your needs with an appropriate machine type. You can define multiple instance templates with varying machine type sizes in your Nextflow configuration using the `machineType` [process directive](https://docs.seqera.io/nextflow/google#process-definition) (e.g., `process.machineType = 'template://my-template-name'`). You can use [process selectors](https://docs.seqera.io/nextflow/config#config-process-selectors) to assign separate templates to each of your processes. ::: Select **Create** to finalize the compute environment setup. @@ -244,7 +244,7 @@ See [Launch pipelines](../launch/launchpad) to start executing workflows in your [create-sa]: https://cloud.google.com/iam/docs/service-accounts-create#creating [get-json]: https://cloud.google.com/iam/docs/keys-list-get#get-key [location]: https://cloud.google.com/compute/docs/regions-zones#available -[wave-docs]: https://www.nextflow.io/docs/latest/wave.html +[wave-docs]: https://docs.seqera.io/nextflow/wave [fusion-docs]: https://docs.seqera.io/fusion [platform-fusion-docs]: ../supported_software/fusion/overview [pre-post-run-scripts]: ../launch/advanced#pre-and-post-run-scripts diff --git a/platform-enterprise_versioned_docs/version-25.3/compute-envs/hpc.md b/platform-enterprise_versioned_docs/version-25.3/compute-envs/hpc.md index 3c18037a1..98cd817b8 100644 --- a/platform-enterprise_versioned_docs/version-25.3/compute-envs/hpc.md +++ b/platform-enterprise_versioned_docs/version-25.3/compute-envs/hpc.md @@ -64,8 +64,8 @@ To create a new **HPC** compute environment: 1. Enter the absolute path of the **Launch directory** to be used on the cluster. If omitted, it will be the same as the work directory. 1. Enter the **Login hostname**. This is usually the hostname or public IP address of the cluster's login node. -1. Enter the **Head queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will be submitted. -1. Enter the **Compute queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will submit tasks. +1. Enter the **Head queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will be submitted. +1. Enter the **Compute queue name**. This is the [default](https://docs.seqera.io/nextflow/process#queue) cluster queue to which the Nextflow job will submit tasks. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. diff --git a/platform-enterprise_versioned_docs/version-25.3/compute-envs/overview.md b/platform-enterprise_versioned_docs/version-25.3/compute-envs/overview.md index b888a301c..4d3a1d6cb 100644 --- a/platform-enterprise_versioned_docs/version-25.3/compute-envs/overview.md +++ b/platform-enterprise_versioned_docs/version-25.3/compute-envs/overview.md @@ -49,8 +49,8 @@ Some important considerations: - Seqera only supports NVIDIA GPUs. Select instances with NVIDIA GPUs for your GPU-dependent processes. - The **Enable GPUs** setting causes Batch Forge to specify the most current [AWS-recommended GPU-optimized ECS AMI](https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ecs-optimized_AMI.html) as the EC2 fleet AMI when creating the compute environment. This setting can be overridden by **AMI ID** in the advanced options. - The **Enable GPUs** setting alone does not deploy GPU instances in your compute environment. You must still specify GPU-enabled instance types in the **Advanced options > Instance types** field. -- Your Nextflow script must include [accelerator directives](https://www.nextflow.io/docs/latest/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. -- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: +- Your Nextflow script must include [accelerator directives](https://docs.seqera.io/nextflow/process.html?highlight=accelerator#accelerator) to use the provisioned GPUs. +- The NVIDIA Container Runtime uses [environment variables](https://github.com/NVIDIA/nvidia-container-runtime#environment-variables-oci-spec) in container images to specify a GPU accelerated container. These variables should be included in the [`containerOptions`](https://docs.seqera.io/nextflow/process#process-containeroptions) directive for each GPU-dependent process in your Nextflow script. The `containerOptions` directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named `UseGPU` via configuration: ```groovy process { diff --git a/platform-enterprise_versioned_docs/version-25.3/credentials/aws_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.3/credentials/aws_registry_credentials.md index 337f109ec..15f17af93 100644 --- a/platform-enterprise_versioned_docs/version-25.3/credentials/aws_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.3/credentials/aws_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [aws, ecr, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see [the Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-25.3/credentials/azure_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.3/credentials/azure_registry_credentials.md index 47e0184b7..a35a15b43 100644 --- a/platform-enterprise_versioned_docs/version-25.3/credentials/azure_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.3/credentials/azure_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [azure, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-25.3/credentials/docker_hub_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.3/credentials/docker_hub_registry_credentials.md index 1c1e376d6..8ce8339a4 100644 --- a/platform-enterprise_versioned_docs/version-25.3/credentials/docker_hub_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.3/credentials/docker_hub_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [docker, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-25.3/credentials/gitea_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.3/credentials/gitea_registry_credentials.md index 68942d36e..83f4668ed 100644 --- a/platform-enterprise_versioned_docs/version-25.3/credentials/gitea_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.3/credentials/gitea_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [gitea, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). Gitea container registries support [authentication][gitea-auth] using a personal access token. Use your personal access token as your password when you create your Gitea container registry credentials in Seqera. diff --git a/platform-enterprise_versioned_docs/version-25.3/credentials/github_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.3/credentials/github_registry_credentials.md index e69de52aa..f24937d55 100644 --- a/platform-enterprise_versioned_docs/version-25.3/credentials/github_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.3/credentials/github_registry_credentials.md @@ -5,7 +5,7 @@ date: "15 Dec 2023" tags: [github, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). GitHub Packages only supports [authentication][github-pat] using a personal access token (classic). Use your personal access token as your password when you create your GitHub container registry credentials in Seqera. diff --git a/platform-enterprise_versioned_docs/version-25.3/credentials/gitlab_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.3/credentials/gitlab_registry_credentials.md index 39a91e0bc..ff4e1ace0 100644 --- a/platform-enterprise_versioned_docs/version-25.3/credentials/gitlab_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.3/credentials/gitlab_registry_credentials.md @@ -5,7 +5,7 @@ date: "2023-12-15" tags: [gitlab, registry, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). If your organization enabled two-factor authentication (2FA) for your GitLab organization or project, you must use your [personal access token][gitlab-pat] as your password when you create your [GitLab container registry credentials][gitlab-cr]. diff --git a/platform-enterprise_versioned_docs/version-25.3/credentials/google_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.3/credentials/google_registry_credentials.md index f6487e1e1..f580d30e1 100644 --- a/platform-enterprise_versioned_docs/version-25.3/credentials/google_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.3/credentials/google_registry_credentials.md @@ -5,7 +5,7 @@ date: "2023-04-21" tags: [google, container, registry, artifact, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-25.3/credentials/quay_registry_credentials.md b/platform-enterprise_versioned_docs/version-25.3/credentials/quay_registry_credentials.md index 9a160b73d..93563fa32 100644 --- a/platform-enterprise_versioned_docs/version-25.3/credentials/quay_registry_credentials.md +++ b/platform-enterprise_versioned_docs/version-25.3/credentials/quay_registry_credentials.md @@ -5,7 +5,7 @@ date: "21 Apr 2023" tags: [quay, credentials] --- -From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/wave.html). +From version 22.3, Seqera Platform supports the configuration of credentials for the Nextflow Wave container service to authenticate to private and public container registries. For more information on Wave containers, see the [Nextflow documentation](https://docs.seqera.io/nextflow/wave). :::note Container registry credentials are only used by the Wave container service. Add `wave { enabled=true }` to the **Nextflow config** field on the launch page, or to your `nextflow.config` file, for your pipeline execution to use Wave containers. diff --git a/platform-enterprise_versioned_docs/version-25.3/enterprise/advanced-topics/manual-azure-batch-setup.md b/platform-enterprise_versioned_docs/version-25.3/enterprise/advanced-topics/manual-azure-batch-setup.md index 4e7c9894d..473311c80 100644 --- a/platform-enterprise_versioned_docs/version-25.3/enterprise/advanced-topics/manual-azure-batch-setup.md +++ b/platform-enterprise_versioned_docs/version-25.3/enterprise/advanced-topics/manual-azure-batch-setup.md @@ -320,7 +320,7 @@ Select **Launch** next to the `hello-world-autopool-low-priority` pipeline in yo Seqera can utilize an Azure Entra service principal to authenticate and access Azure Batch for job execution and Azure Storage for data management, and Nextflow can authenticate to Azure services using a managed identity. This method offers enhanced security compared to access keys, but must run on Azure infrastructure. -See [Microsoft Entra](https://www.nextflow.io/docs/latest/azure.html#microsoft-entra) in the Nextflow documentation for more information. +See [Microsoft Entra](https://docs.seqera.io/nextflow/azure#microsoft-entra) in the Nextflow documentation for more information. #### Create a service principal for Seqera to use for authentication @@ -340,7 +340,7 @@ In Seqera: Back in the Azure Portal: 1. [Create a managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-manage-user-assigned-managed-identities?pivots=identity-mi-methods-azp) -1. [Assign the relevant roles to the managed identity](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current). See [Required role assignments](https://www.nextflow.io/docs/latest/azure.html#required-role-assignments) for Nextflow requirements. +1. [Assign the relevant roles to the managed identity](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current). See [Required role assignments](https://docs.seqera.io/nextflow/azure#required-role-assignments) for Nextflow requirements. 1. Note the managed identity client ID for later. 1. In the Azure Portal, go to the Batch account you created earlier. 1. Go to the **Pools** tab and find the pool called `tower-pool-${id}`, where `${id}` is the ID of the head node pool created earlier. @@ -481,6 +481,6 @@ If you wish to keep the Azure resources, you can remove each pool within a Batch [install-azure-cli]: https://learn.microsoft.com/en-us/cli/azure/install-azure-cli [install-seqera-cli]: /platform-cli/installation -[nextflow-working-directory]: https://www.nextflow.io/docs/latest/cache-and-resume.html#work-directory +[nextflow-working-directory]: https://docs.seqera.io/nextflow/cache-and-resume#work-directory [create-org-workspace]: ../../getting-started/workspace-setup [add-pipeline]: ../../getting-started/quickstart-demo/add-pipelines#add-from-the-launchpad diff --git a/platform-enterprise_versioned_docs/version-25.3/enterprise/configuration/wave.md b/platform-enterprise_versioned_docs/version-25.3/enterprise/configuration/wave.md index b84fe0534..8d84565f1 100644 --- a/platform-enterprise_versioned_docs/version-25.3/enterprise/configuration/wave.md +++ b/platform-enterprise_versioned_docs/version-25.3/enterprise/configuration/wave.md @@ -79,5 +79,5 @@ See the [Wave documentation](https://docs.seqera.io/wave) for installation and c ## Additional resources - [Wave documentation](https://docs.seqera.io/wave) -- [Nextflow Wave integration](https://www.nextflow.io/docs/latest/wave.html) +- [Nextflow Wave integration](https://docs.seqera.io/nextflow/wave) - [Seqera Containers](https://seqera.io/containers/) - Free community container registry diff --git a/platform-enterprise_versioned_docs/version-25.3/getting-started/deployment-options.md b/platform-enterprise_versioned_docs/version-25.3/getting-started/deployment-options.md index 7fe24fd1a..49e4f2f87 100644 --- a/platform-enterprise_versioned_docs/version-25.3/getting-started/deployment-options.md +++ b/platform-enterprise_versioned_docs/version-25.3/getting-started/deployment-options.md @@ -86,5 +86,5 @@ If you have an existing environment where you run Nextflow directly, you can sti You can now monitor your workflow runs in the Seqera interface. To configure and execute Nextflow pipelines in cloud environments, see [compute environments](../compute-envs/overview). :::tip -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/config.html?highlight=tower#scope-tower) for further run configuration options using Nextflow configuration files. ::: diff --git a/platform-enterprise_versioned_docs/version-25.3/getting-started/proteinfold.md b/platform-enterprise_versioned_docs/version-25.3/getting-started/proteinfold.md index 29a25a09d..7cdcc1ee8 100644 --- a/platform-enterprise_versioned_docs/version-25.3/getting-started/proteinfold.md +++ b/platform-enterprise_versioned_docs/version-25.3/getting-started/proteinfold.md @@ -185,7 +185,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL: `https://github.com/nf-core/proteinfold`. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name: `1.1.1`. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. Benchmarking runs for this guide used nf-core profiles with included test datasets — `test_full_alphafold2_multimer` for Alphafold2 and `test_full_alphafold2_multimer` for Colabfold. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-enterprise_versioned_docs/version-25.3/getting-started/quickstart-demo/launch-pipelines.md b/platform-enterprise_versioned_docs/version-25.3/getting-started/quickstart-demo/launch-pipelines.md index ddbc10c08..5615cc7a3 100644 --- a/platform-enterprise_versioned_docs/version-25.3/getting-started/quickstart-demo/launch-pipelines.md +++ b/platform-enterprise_versioned_docs/version-25.3/getting-started/quickstart-demo/launch-pipelines.md @@ -49,7 +49,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc :::info See [Git revision management](../../pipelines/revision.md) for more information on **Commit ID**, **Pull latest**, and **Revision** behavior. ::: -- (*Optional*) **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. +- (*Optional*) **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - (*Optional*) **Labels**: Assign new or existing [labels](../../labels/overview) to the run. - **Compute environment**: Select an existing workspace [compute environment](../../compute-envs/overview). diff --git a/platform-enterprise_versioned_docs/version-25.3/getting-started/rnaseq.md b/platform-enterprise_versioned_docs/version-25.3/getting-started/rnaseq.md index 312895d63..4af640987 100644 --- a/platform-enterprise_versioned_docs/version-25.3/getting-started/rnaseq.md +++ b/platform-enterprise_versioned_docs/version-25.3/getting-started/rnaseq.md @@ -196,7 +196,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc - **Pipeline to launch**: The pipeline Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. - **Revision number**: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited. -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: An identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: Your AWS Batch compute environment. diff --git a/platform-enterprise_versioned_docs/version-25.3/launch/advanced.md b/platform-enterprise_versioned_docs/version-25.3/launch/advanced.md index 714f50a43..7a6060212 100644 --- a/platform-enterprise_versioned_docs/version-25.3/launch/advanced.md +++ b/platform-enterprise_versioned_docs/version-25.3/launch/advanced.md @@ -10,7 +10,7 @@ You can modify the configuration and execution of a pipeline with advanced launc ### Nextflow config file -Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://www.nextflow.io/docs/latest/config.html#config-syntax). +Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax). For example, modify the **manifest** section to give the pipeline a name and description that will show up in the Seqera monitoring section: @@ -127,7 +127,7 @@ Instruct Nextflow to pull the latest pipeline version from the Git repository. T ### Stub run -Replace Nextflow process commands with command [stubs](https://www.nextflow.io/docs/latest/process.html#stub), where defined, before execution. +Replace Nextflow process commands with command [stubs](https://docs.seqera.io/nextflow/process#stub), where defined, before execution. ### Main script diff --git a/platform-enterprise_versioned_docs/version-25.3/launch/cache-resume.mdx b/platform-enterprise_versioned_docs/version-25.3/launch/cache-resume.mdx index 558b0d2ad..ef47bd4d2 100644 --- a/platform-enterprise_versioned_docs/version-25.3/launch/cache-resume.mdx +++ b/platform-enterprise_versioned_docs/version-25.3/launch/cache-resume.mdx @@ -8,13 +8,13 @@ tags: [cache, launch, resume, relaunch] import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; -Nextflow maintains a [cache](https://www.nextflow.io/docs/latest/cache-and-resume.html) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. +Nextflow maintains a [cache](https://docs.seqera.io/nextflow/cache-and-resume) directory where it stores the intermediate results and metadata from workflow runs. Workflows executed in Seqera Platform use this caching mechanism to enable users to relaunch or resume failed or otherwise interrupted runs as needed. This eliminates the need to re-execute successfully completed tasks when a workflow is executed again due to task failures or other interruptions. ## Cache directory -Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://www.nextflow.io/docs/latest/cache-and-resume.html#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. +Nextflow stores all task executions to the task cache automatically, whether or not the resume or relaunch option is used. This makes it possible to resume or relaunch runs later if needed. Platform HPC and local compute environments use the default Nextflow cache directory (`.nextflow/cache`) to store the task cache. Cloud compute environments use the [cloud cache](https://docs.seqera.io/nextflow/cache-and-resume#cache-stores) mechanism to store the task cache in a sub-folder of the pipeline work directory. -To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://www.nextflow.io/docs/latest/process.html#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). +To override the default cloud cache location in cloud compute environments, specify an alternate directory with the [cache](https://docs.seqera.io/nextflow/process#process-cache) directive in your Nextflow configuration file (either in the **Advanced options > Nextflow config file** field on the launch form, or in the `nextflow.config` file in your pipeline repository). @@ -108,7 +108,7 @@ Kubernetes compute environments do not use cloud cache by default. To specify a Google Cloud Storage 1. See [these instructions](../compute-envs/google-cloud-batch#iam) to set up IAM and create a JSON key file for the custom service account with permissions to your Google Cloud storage account. - 2. If you run the [gcloud CLI authentication flow](https://nextflow.io/docs/edge/google.html#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. + 2. If you run the [gcloud CLI authentication flow](https://docs.seqera.io/nextflow/google#credentials) with `gcloud auth application-default login`, your Application Default Credentials are written to `$HOME/.config/gcloud/application_default_credentials.json` and picked up by Nextflow automatically. Otherwise, declare the `GOOGLE_APPLICATION_CREDENTIALS` environment variable explicitly with the local path to your service account credentials file created in the previous step. 3. Add the following to the **Nextflow Config file** field when you [launch](../launch/launchpad#launch-form) your pipeline: ```groovy diff --git a/platform-enterprise_versioned_docs/version-25.3/launch/launchpad.md b/platform-enterprise_versioned_docs/version-25.3/launch/launchpad.md index 7189fe720..0c2310afa 100644 --- a/platform-enterprise_versioned_docs/version-25.3/launch/launchpad.md +++ b/platform-enterprise_versioned_docs/version-25.3/launch/launchpad.md @@ -33,7 +33,7 @@ The launch form accepts URL query parameters. See [Populate launch form with URL - **Pipeline to launch**: A Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. Private repositories require [access credentials](../credentials/overview). :::note - Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://www.nextflow.io/docs/latest/sharing.html) in the Nextflow docs for more details. + Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview) in the Seqera docs and [Pipeline sharing](https://docs.seqera.io/nextflow/sharing) in the Nextflow docs for more details. ::: - **Revision**: A valid repository commit ID, tag, or branch name. Determines the version of the pipeline to launch. - **Commit ID**: Pin pipeline revision to the most recent HEAD commit ID. If no commit ID is pinned, the latest revision of the repository branch or tag is used. @@ -41,7 +41,7 @@ The launch form accepts URL query parameters. See [Populate launch form with URL :::info See [Git revision management](../pipelines/revision.md) for more information on **Commit ID**, **Pull latest**, and **Revision** behavior. ::: -- **Config profiles**: One or more [configuration profile](https://www.nextflow.io/docs/latest/config.html#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. +- **Config profiles**: One or more [configuration profile](https://docs.seqera.io/nextflow/config#config-profiles) names to use for the execution. Config profiles must be defined in the `nextflow.config` file in the pipeline repository. - **Workflow run name**: A unique identifier for the run, pre-filled with a random name. This can be customized. - **Labels**: Assign new or existing [labels](../labels/overview) to the run. - **Compute environment**: The [compute environment](../compute-envs/overview) where the run will be launched. @@ -116,7 +116,7 @@ Use resource labels to tag the computing resources created during the workflow e Secrets are used to store keys and tokens used by workflow tasks to interact with external systems. Enter the names of any stored user or workspace secrets required for the workflow execution. :::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: #### Advanced options diff --git a/platform-enterprise_versioned_docs/version-25.3/monitoring/overview.md b/platform-enterprise_versioned_docs/version-25.3/monitoring/overview.md index 53b40928e..6a9e1b66e 100644 --- a/platform-enterprise_versioned_docs/version-25.3/monitoring/overview.md +++ b/platform-enterprise_versioned_docs/version-25.3/monitoring/overview.md @@ -13,7 +13,7 @@ The **Runs** tab contains all previous runs in the workspace. Each new or resume - `submitted`: Pending execution - `running`: Running - `succeeded`: Completed successfully -- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://www.nextflow.io/docs/latest/process.html#errorstrategy) +- `failed`: Successfully executed, where at least one task failed with a `terminate` [error strategy](https://docs.seqera.io/nextflow/process#errorstrategy) - `cancelled`: Stopped manually during execution - `unknown`: Indeterminate status diff --git a/platform-enterprise_versioned_docs/version-25.3/pipelines/overview.md b/platform-enterprise_versioned_docs/version-25.3/pipelines/overview.md index afc7283a0..dac5e2e68 100644 --- a/platform-enterprise_versioned_docs/version-25.3/pipelines/overview.md +++ b/platform-enterprise_versioned_docs/version-25.3/pipelines/overview.md @@ -11,7 +11,7 @@ When you add a pipeline to Seqera, you define: - The pipeline Git repository and [revision](./revision.md) (branch, tag, or commit) - [Compute environment](../compute-envs/overview.md) for execution -- Pipeline parameters and [configuration profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) +- Pipeline parameters and [configuration profiles](https://docs.seqera.io/nextflow/config#config-profiles) - (Optional) [Labels](../labels/overview.md), [resource labels](../resource-labels/overview.md), and [secrets](../secrets/overview.md) - (Optional) [Pre-run and post-run](../launch/advanced.md#pre-and-post-run-scripts) bash scripts that execute in your compute environment diff --git a/platform-enterprise_versioned_docs/version-25.3/platform-enterprise.md b/platform-enterprise_versioned_docs/version-25.3/platform-enterprise.md index e32595db8..bc837db8f 100644 --- a/platform-enterprise_versioned_docs/version-25.3/platform-enterprise.md +++ b/platform-enterprise_versioned_docs/version-25.3/platform-enterprise.md @@ -29,4 +29,4 @@ Request a [**demo**](https://seqera.io/demo "Seqera Enterprise Demo") to explore Nextflow is both a programming workflow language and an execution runtime that supports a wide range of execution platforms, including popular traditional grid scheduling systems such as Slurm and IBM LSF, and cloud services such as AWS, Azure, and Google Cloud Batch. -See the [Nextflow documentation](https://www.nextflow.io/docs/latest/) to learn more. +See the [Nextflow documentation](https://docs.seqera.io/nextflow/) to learn more. diff --git a/platform-enterprise_versioned_docs/version-25.3/reports/overview.md b/platform-enterprise_versioned_docs/version-25.3/reports/overview.md index c4ba99b1c..59db26855 100644 --- a/platform-enterprise_versioned_docs/version-25.3/reports/overview.md +++ b/platform-enterprise_versioned_docs/version-25.3/reports/overview.md @@ -82,10 +82,10 @@ By default, the MIME type is deduced from the file extension, so you don't need Nextflow can generate a number of built-in reports: -- [Execution report](https://nextflow.io/docs/latest/tracing.html#execution-report) -- [Execution timeline](https://nextflow.io/docs/latest/tracing.html#timeline-report) -- [Trace file](https://nextflow.io/docs/latest/tracing.html#trace-report) -- [Workflow diagram](https://nextflow.io/docs/latest/tracing.html#dag-visualisation) (i.e. DAG) +- [Execution report](https://docs.seqera.io/nextflow/tracing#execution-report) +- [Execution timeline](https://docs.seqera.io/nextflow/tracing#timeline-report) +- [Trace file](https://docs.seqera.io/nextflow/tracing#trace-report) +- [Workflow diagram](https://docs.seqera.io/nextflow/tracing#dag-visualisation) (i.e. DAG) In Nextflow version 24.03.0-edge and later, these reports can be included as pipeline reports in Seqera Platform. Specify them in `tower.yml` like any other file: diff --git a/platform-enterprise_versioned_docs/version-25.3/secrets/overview.md b/platform-enterprise_versioned_docs/version-25.3/secrets/overview.md index e6498a5fd..c5c1d130a 100644 --- a/platform-enterprise_versioned_docs/version-25.3/secrets/overview.md +++ b/platform-enterprise_versioned_docs/version-25.3/secrets/overview.md @@ -31,12 +31,12 @@ Secrets defined by a user have higher priority and will override any secrets wit ## Use secrets in workflows -When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://www.nextflow.io/docs/edge/secrets.html#process-secrets) for more information. +When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See [Nextflow secrets](https://docs.seqera.io/nextflow/secrets) for more information. Secrets are automatically deleted from the secret manager when the pipeline completes, successfully or unsuccessfully. :::note -In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://www.nextflow.io/docs/latest/aws.html#custom-job-definition). +In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a [custom job definition](https://docs.seqera.io/nextflow/aws#custom-job-definition). ::: ## AWS Secrets Manager integration diff --git a/platform-enterprise_versioned_docs/version-25.3/supported_software/dragen/overview.md b/platform-enterprise_versioned_docs/version-25.3/supported_software/dragen/overview.md index 90b17c409..0ab3e9023 100644 --- a/platform-enterprise_versioned_docs/version-25.3/supported_software/dragen/overview.md +++ b/platform-enterprise_versioned_docs/version-25.3/supported_software/dragen/overview.md @@ -80,7 +80,7 @@ See the [dragen.nf](https://github.com/seqeralabs/nf-dragen/blob/master/modules/ } ``` - See the [Nextflow label docs](https://www.nextflow.io/docs/latest/process.html?highlight=label#label) for more information. + See the [Nextflow label docs](https://docs.seqera.io/nextflow/process.html?highlight=label#label) for more information. 2. Define secrets in Seqera: diff --git a/platform-enterprise_versioned_docs/version-25.3/troubleshooting_and_faqs/azure_troubleshooting.md b/platform-enterprise_versioned_docs/version-25.3/troubleshooting_and_faqs/azure_troubleshooting.md index bf88be612..62b10f218 100644 --- a/platform-enterprise_versioned_docs/version-25.3/troubleshooting_and_faqs/azure_troubleshooting.md +++ b/platform-enterprise_versioned_docs/version-25.3/troubleshooting_and_faqs/azure_troubleshooting.md @@ -16,12 +16,12 @@ The default Azure Batch implementation in Seqera Platform uses a single pool for - One [Low priority](https://learn.microsoft.com/en-us/azure/batch/batch-spot-vms#differences-between-spot-and-low-priority-vms) :::note -Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://www.nextflow.io/docs/latest/azure.html#requirements-on-pre-existing-named-pools). +Both pools must meet the requirements of a pre-existing pool as detailed in the [Nextflow documentation](https://docs.seqera.io/nextflow/azure#requirements-on-pre-existing-named-pools). ::: 2. Create a manual [Azure Batch](../compute-envs/azure-batch#manual) compute environment in Seqera Platform. 3. In **Compute pool name**, specify your dedicated Batch pool. -4. Specify the Low priority pool using the `process.queue` [directive](https://www.nextflow.io/docs/latest/process.html#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. +4. Specify the Low priority pool using the `process.queue` [directive](https://docs.seqera.io/nextflow/process#queue) in your `nextflow.config` file either via the launch form, or your pipeline repository's `nextflow.config` file. ### Azure Kubernetes Service (AKS) diff --git a/platform-enterprise_versioned_docs/version-25.3/troubleshooting_and_faqs/nextflow.md b/platform-enterprise_versioned_docs/version-25.3/troubleshooting_and_faqs/nextflow.md index e8003814e..89d0feeba 100644 --- a/platform-enterprise_versioned_docs/version-25.3/troubleshooting_and_faqs/nextflow.md +++ b/platform-enterprise_versioned_docs/version-25.3/troubleshooting_and_faqs/nextflow.md @@ -20,7 +20,7 @@ To minimize disruption on existing pipelines, version 22.1.x and later are confi **Invoke Nextflow CLI run arguments during Seqera launch** -From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://www.nextflow.io/docs/latest/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): +From [Nextflow v22.09.1-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.09.1-edge), you can specify [Nextflow CLI run arguments](https://docs.seqera.io/nextflow/cli.html?highlight=dump#run) when invoking a pipeline from Seqera. Set the `NXF_CLI_OPTS` environment variable using a [pre-run script](../launch/advanced#pre-and-post-run-scripts): ``` export NXF_CLI_OPTS='-dump-hashes' @@ -44,7 +44,7 @@ Currently, you can resolve this by creating empty `main.nf` and `nextflow.config **Use multiple Nextflow configuration files for different environments** -The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) in the main `nextflow.config`. +The main `nextflow.config` file is always imported by default. Instead of managing multiple `nextflow.config` files (each customized for an environment), you can create unique environment config files and import them as [config profiles](https://docs.seqera.io/nextflow/config#config-profiles) in the main `nextflow.config`. Example: @@ -152,7 +152,7 @@ process.afterScript = 'sleep 60' **Jobs remain in RUNNING status when a pipeline run is canceled** -Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: +Your instance's behavior when canceling a run depends on the Nextflow [`errorStrategy`](https://docs.seqera.io/nextflow/process#errorstrategy) defined in your process script. If the process `errorStrategy` is set to `finish`, an orderly pipeline shutdown is initiated when you cancel (or otherwise interrupt) a run. This instructs Nextflow to wait for the completion of any submitted jobs. To ensure that all jobs are terminated when your run is canceled, set `errorStrategy` to `terminate` in your Nextflow config. For example: ``` process terminateError { @@ -196,7 +196,7 @@ The Groovy shell used by Nextflow to execute your workflow has a hard limit on s 1. Remove any unnecessary code or comments from the script. 2. Move long script bodies into a separate script file in the pipeline `/bin` directory. -3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://www.nextflow.io/docs/latest/dsl2.html#modules). +3. Consider using DSL2 so you can move each function, process, and workflow definition into its own script and include these scripts as [modules](https://docs.seqera.io/nextflow/dsl2#modules). ### Nextflow Launcher diff --git a/platform-enterprise_versioned_docs/version-25.3/troubleshooting_and_faqs/troubleshooting.md b/platform-enterprise_versioned_docs/version-25.3/troubleshooting_and_faqs/troubleshooting.md index 019f2dc62..b044e6068 100644 --- a/platform-enterprise_versioned_docs/version-25.3/troubleshooting_and_faqs/troubleshooting.md +++ b/platform-enterprise_versioned_docs/version-25.3/troubleshooting_and_faqs/troubleshooting.md @@ -47,7 +47,7 @@ This error can occur if you execute a DSL1-based Nextflow workflow using [Nextfl The `sleep` commands in your Nextflow workflows may differ in behavior depending on where they are: - If used within an `errorStrategy` block, the Groovy sleep function will be used (which takes its value in milliseconds). -- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://www.nextflow.io/docs/latest/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. +- If used within a process script block, that language's sleep binary/method will be used. For example, [this bash script](https://docs.seqera.io/nextflow/metrics.html?highlight=sleep) uses the bash sleep binary, which takes its value in seconds. **Large number of batch job definitions**