From cc31edd960d0451b8628797fea039237a92e8b17 Mon Sep 17 00:00:00 2001 From: Llewellyn vd Berg <113503285+llewellyn-sl@users.noreply.github.com> Date: Sun, 11 May 2025 12:37:21 +0200 Subject: [PATCH 1/4] Update docs to MD files to fix build issues --- docs/{api.mdx => api.md} | 0 docs/cli/{index.mdx => index.md} | 0 docs/cli/{reference.mdx => reference.md} | 2 +- docs/{configuration.mdx => configuration.md} | 0 docs/{faq.mdx => faq.md} | 0 docs/{get-started.mdx => get-started.md} | 6 +++--- docs/{index.mdx => index.md} | 16 ++++++++-------- docs/{metrics.mdx => metrics.md} | 0 docs/{nextflow.mdx => nextflow.md} | 2 +- docs/{provisioning.mdx => provisioning.md} | 0 docs/{troubleshoot.mdx => troubleshoot.md} | 0 11 files changed, 13 insertions(+), 13 deletions(-) rename docs/{api.mdx => api.md} (100%) rename docs/cli/{index.mdx => index.md} (100%) rename docs/cli/{reference.mdx => reference.md} (99%) rename docs/{configuration.mdx => configuration.md} (100%) rename docs/{faq.mdx => faq.md} (100%) rename docs/{get-started.mdx => get-started.md} (99%) rename docs/{index.mdx => index.md} (93%) rename docs/{metrics.mdx => metrics.md} (100%) rename docs/{nextflow.mdx => nextflow.md} (99%) rename docs/{provisioning.mdx => provisioning.md} (100%) rename docs/{troubleshoot.mdx => troubleshoot.md} (100%) diff --git a/docs/api.mdx b/docs/api.md similarity index 100% rename from docs/api.mdx rename to docs/api.md diff --git a/docs/cli/index.mdx b/docs/cli/index.md similarity index 100% rename from docs/cli/index.mdx rename to docs/cli/index.md diff --git a/docs/cli/reference.mdx b/docs/cli/reference.md similarity index 99% rename from docs/cli/reference.mdx rename to docs/cli/reference.md index fae9c3cb1..e6a586880 100644 --- a/docs/cli/reference.mdx +++ b/docs/cli/reference.md @@ -54,7 +54,7 @@ With the Wave CLI you can build Docker and Singularity containers from a variety The following sections describe several common usage cases. To get started by creating an example Nextflow pipeline that uses Wave CLI, see [Get started][start]. -[start]: ../get-started.mdx#wave-cli +[start]: ../get-started#wave-cli ### Augment a container with a directory diff --git a/docs/configuration.mdx b/docs/configuration.md similarity index 100% rename from docs/configuration.mdx rename to docs/configuration.md diff --git a/docs/faq.mdx b/docs/faq.md similarity index 100% rename from docs/faq.mdx rename to docs/faq.md diff --git a/docs/get-started.mdx b/docs/get-started.md similarity index 99% rename from docs/get-started.mdx rename to docs/get-started.md index 08c63b587..9a9ff3087 100644 --- a/docs/get-started.mdx +++ b/docs/get-started.md @@ -374,6 +374,6 @@ Reneechester, AK 75644 [Podman]: https://podman.io/docs/installation [Docker Desktop]: https://www.docker.com/products/docker-desktop/ -[wave-build]: ./cli/reference.mdx#build-a-container -[nf-config]: ./nextflow.mdx#configuration-options -[wave-cli]: ./cli/index.mdx +[wave-build]: ./cli/reference#build-a-container +[nf-config]: ./nextflow#configuration-options +[wave-cli]: ./cli/index diff --git a/docs/index.mdx b/docs/index.md similarity index 93% rename from docs/index.mdx rename to docs/index.md index a9dc1017f..8775bb1ba 100644 --- a/docs/index.mdx +++ b/docs/index.md @@ -16,9 +16,9 @@ To get started with Wave: Wave is also available as hosted service on [Seqera Platform](https://cloud.seqera.io/). For Seqera Enterprise customers, a licensed self-hosted Wave solution is also available. Contact us [contact us](https://seqera.io/contact-us/) for more information. ::: -[started]: ./get-started.mdx -[nf]: ./nextflow.mdx -[cli]: ./cli/index.mdx +[started]: ./get-started +[nf]: ./nextflow +[cli]: ./cli/index ## Wave features @@ -28,13 +28,13 @@ Wave is also available as hosted service on [Seqera Platform](https://cloud.seqe Wave integrates with [Seqera Platform credentials management][private] enabling seamless access and publishing to private registries. -[private]: ./nextflow.mdx#access-private-container-repositories +[private]: ./nextflow#access-private-container-repositories #### Seqera Containers - The community container registry [Seqera Containers] is a free to use service operated for the community by Seqera. -It uses Wave to build images from Conda / PyPI packages on demand, either through the [web interface](https://seqera.io/containers/) or using the [Wave CLI](./cli/index.mdx) / [Nextflow integration](./nextflow.mdx). +It uses Wave to build images from Conda / PyPI packages on demand, either through the [web interface](https://seqera.io/containers/) or using the [Wave CLI](./cli/index) / [Nextflow integration](./nextflow). These images are cached and hosted permanently, being served through a [Docker Distribution][docker] registry and hosted on AWS infrastructure. Images are cached and served via Cloudflare CDN. @@ -52,14 +52,14 @@ Seqera Containers does not work with custom container files, augmentation, or au Wave offers a flexible approach to container image management. It allows you to [dynamically add custom layers][augment] to existing docker images, creating new images tailored to your specific needs. Any existing container can be extended without rebuilding it. You can add user-provided content such as custom scripts and logging agents, providing greater flexibility in the container’s configuration. -[augment]: ./provisioning.mdx#container-augmentation +[augment]: ./provisioning#container-augmentation ### Conda-based containers Package management systems such as Conda and Bioconda simplify the installation of scientific software. Wave enables dynamic provisioning of container images from any Conda or Bioconda recipe. Just [declare the Conda packages][conda] in your Nextflow pipeline and Wave will assemble the required container. -[conda]: ./nextflow.mdx#build-conda-based-containers +[conda]: ./nextflow#build-conda-based-containers ### Singularity containers @@ -71,7 +71,7 @@ The advantage of this approach is that Singularity and Apptainer engines can pul Considering the Singularity image format's peculiarities, Wave's freeze mode is mandatory when provisioning Singularity images. ::: -[singularity]: ./nextflow.mdx#build-singularity-containers +[singularity]: ./nextflow#build-singularity-containers ### Deploying containers across multi-clouds diff --git a/docs/metrics.mdx b/docs/metrics.md similarity index 100% rename from docs/metrics.mdx rename to docs/metrics.md diff --git a/docs/nextflow.mdx b/docs/nextflow.md similarity index 99% rename from docs/nextflow.mdx rename to docs/nextflow.md index 7c2cf6f2b..e292d4c82 100644 --- a/docs/nextflow.mdx +++ b/docs/nextflow.md @@ -27,7 +27,7 @@ For the entire list of configuration options, see [Configuration options](#confi The following sections describe several common usage cases. To get started by creating an example pipeline that uses Wave, see [Get started][start]. -[start]: ./get-started.mdx#nextflow +[start]: ./get-started#nextflow ### Access private container repositories diff --git a/docs/provisioning.mdx b/docs/provisioning.md similarity index 100% rename from docs/provisioning.mdx rename to docs/provisioning.md diff --git a/docs/troubleshoot.mdx b/docs/troubleshoot.md similarity index 100% rename from docs/troubleshoot.mdx rename to docs/troubleshoot.md From 6e4c28197eec7a1708fc0c74c53849ddf9afd467 Mon Sep 17 00:00:00 2001 From: Llewellyn vd Berg <113503285+llewellyn-sl@users.noreply.github.com> Date: Wed, 25 Jun 2025 11:50:31 +0200 Subject: [PATCH 2/4] Convert MDX to MD --- docs/{db-migration.mdx => db-migration.md} | 2 +- docs/{wave-lite.mdx => wave-lite.md} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename docs/{db-migration.mdx => db-migration.md} (97%) rename docs/{wave-lite.mdx => wave-lite.md} (100%) diff --git a/docs/db-migration.mdx b/docs/db-migration.md similarity index 97% rename from docs/db-migration.mdx rename to docs/db-migration.md index db74ea0fd..66e05ad04 100644 --- a/docs/db-migration.mdx +++ b/docs/db-migration.md @@ -1,7 +1,7 @@ # Wave Database Migration from SurrealDB to PostgreSQL ## Pre-requisites -- Install [wave-cli] (https://github.com/seqeralabs/wave-cli) +- Install [wave-cli](https://github.com/seqeralabs/wave-cli) - Ensure you have a PostgreSQL database set up and accessible from wave. ## Migration Steps diff --git a/docs/wave-lite.mdx b/docs/wave-lite.md similarity index 100% rename from docs/wave-lite.mdx rename to docs/wave-lite.md From 6823e9aa03b4ead8b344b4ff9a4283b25183c3ad Mon Sep 17 00:00:00 2001 From: Llewellyn vd Berg <113503285+llewellyn-sl@users.noreply.github.com> Date: Sun, 11 May 2025 12:37:21 +0200 Subject: [PATCH 3/4] Update docs to MD files to fix build issues --- docs/{api.mdx => api.md} | 0 docs/cli/{index.mdx => index.md} | 0 docs/cli/{reference.mdx => reference.md} | 2 +- docs/{configuration.mdx => configuration.md} | 0 docs/{faq.mdx => faq.md} | 0 docs/{get-started.mdx => get-started.md} | 6 +++--- docs/{index.mdx => index.md} | 16 ++++++++-------- docs/{metrics.mdx => metrics.md} | 0 docs/{nextflow.mdx => nextflow.md} | 2 +- docs/{provisioning.mdx => provisioning.md} | 0 docs/{troubleshoot.mdx => troubleshoot.md} | 0 11 files changed, 13 insertions(+), 13 deletions(-) rename docs/{api.mdx => api.md} (100%) rename docs/cli/{index.mdx => index.md} (100%) rename docs/cli/{reference.mdx => reference.md} (99%) rename docs/{configuration.mdx => configuration.md} (100%) rename docs/{faq.mdx => faq.md} (100%) rename docs/{get-started.mdx => get-started.md} (99%) rename docs/{index.mdx => index.md} (94%) rename docs/{metrics.mdx => metrics.md} (100%) rename docs/{nextflow.mdx => nextflow.md} (99%) rename docs/{provisioning.mdx => provisioning.md} (100%) rename docs/{troubleshoot.mdx => troubleshoot.md} (100%) diff --git a/docs/api.mdx b/docs/api.md similarity index 100% rename from docs/api.mdx rename to docs/api.md diff --git a/docs/cli/index.mdx b/docs/cli/index.md similarity index 100% rename from docs/cli/index.mdx rename to docs/cli/index.md diff --git a/docs/cli/reference.mdx b/docs/cli/reference.md similarity index 99% rename from docs/cli/reference.mdx rename to docs/cli/reference.md index 302ac1401..ad4cf259a 100644 --- a/docs/cli/reference.mdx +++ b/docs/cli/reference.md @@ -54,7 +54,7 @@ With the Wave CLI you can build Docker and Singularity containers from a variety The following sections describe several common usage cases. To get started by creating an example Nextflow pipeline that uses Wave CLI, see [Get started][start]. -[start]: ../get-started.mdx#wave-cli +[start]: ../get-started#wave-cli ### Augment a container with a directory diff --git a/docs/configuration.mdx b/docs/configuration.md similarity index 100% rename from docs/configuration.mdx rename to docs/configuration.md diff --git a/docs/faq.mdx b/docs/faq.md similarity index 100% rename from docs/faq.mdx rename to docs/faq.md diff --git a/docs/get-started.mdx b/docs/get-started.md similarity index 99% rename from docs/get-started.mdx rename to docs/get-started.md index b1a3553b0..51aeeed67 100644 --- a/docs/get-started.mdx +++ b/docs/get-started.md @@ -375,6 +375,6 @@ Reneechester, AK 75644 [Podman]: https://podman.io/docs/installation [Docker Desktop]: https://www.docker.com/products/docker-desktop/ -[wave-build]: ./cli/reference.mdx#build-a-container -[nf-config]: ./nextflow.mdx#configuration-options -[wave-cli]: ./cli/index.mdx +[wave-build]: ./cli/reference#build-a-container +[nf-config]: ./nextflow#configuration-options +[wave-cli]: ./cli/index diff --git a/docs/index.mdx b/docs/index.md similarity index 94% rename from docs/index.mdx rename to docs/index.md index f0122bb2e..c55f409dc 100644 --- a/docs/index.mdx +++ b/docs/index.md @@ -16,9 +16,9 @@ To get started with Wave: Wave is also available as hosted service on [Seqera Platform](https://cloud.seqera.io/). For Seqera Enterprise customers, a licensed self-hosted Wave solution is also available. Contact us [contact us](https://seqera.io/contact-us/) for more information. ::: -[started]: ./get-started.mdx -[nf]: ./nextflow.mdx -[cli]: ./cli/index.mdx +[started]: ./get-started +[nf]: ./nextflow +[cli]: ./cli/index ## Wave features @@ -28,13 +28,13 @@ Wave is also available as hosted service on [Seqera Platform](https://cloud.seqe Wave integrates with [Seqera Platform credentials management][private] enabling seamless access and publishing to private registries. -[private]: ./nextflow.mdx#access-private-container-repositories +[private]: ./nextflow#access-private-container-repositories #### Seqera Containers - The community container registry [Seqera Containers] is a free to use service operated for the community by Seqera. -It uses Wave to build images from Conda / PyPI packages on demand, either through the [web interface](https://seqera.io/containers/) or using the [Wave CLI](./cli/index.mdx) / [Nextflow integration](./nextflow.mdx). +It uses Wave to build images from Conda / PyPI packages on demand, either through the [web interface](https://seqera.io/containers/) or using the [Wave CLI](./cli/index) / [Nextflow integration](./nextflow). These images are cached and hosted permanently, being served through a [Docker Distribution][docker] registry and hosted on AWS infrastructure. Images are cached and served via Cloudflare CDN. @@ -52,14 +52,14 @@ Seqera Containers does not work with custom container files, augmentation, or au Wave offers a flexible approach to container image management. It allows you to [dynamically add custom layers][augment] to existing docker images, creating new images tailored to your specific needs. Any existing container can be extended without rebuilding it. You can add user-provided content such as custom scripts and logging agents, providing greater flexibility in the container’s configuration. -[augment]: ./provisioning.mdx#container-augmentation +[augment]: ./provisioning#container-augmentation ### Conda-based containers Package management systems such as Conda and Bioconda simplify the installation of scientific software. Wave enables dynamic provisioning of container images from any Conda or Bioconda recipe. Just [declare the Conda packages][conda] in your Nextflow pipeline and Wave will assemble the required container. -[conda]: ./nextflow.mdx#build-conda-based-containers +[conda]: ./nextflow#build-conda-based-containers ### Singularity containers @@ -71,7 +71,7 @@ The advantage of this approach is that Singularity and Apptainer engines can pul Considering the Singularity image format's peculiarities, Wave's freeze mode is mandatory when provisioning Singularity images. ::: -[singularity]: ./nextflow.mdx#build-singularity-containers +[singularity]: ./nextflow#build-singularity-containers ### Deploying containers across multi-clouds diff --git a/docs/metrics.mdx b/docs/metrics.md similarity index 100% rename from docs/metrics.mdx rename to docs/metrics.md diff --git a/docs/nextflow.mdx b/docs/nextflow.md similarity index 99% rename from docs/nextflow.mdx rename to docs/nextflow.md index 7c2cf6f2b..e292d4c82 100644 --- a/docs/nextflow.mdx +++ b/docs/nextflow.md @@ -27,7 +27,7 @@ For the entire list of configuration options, see [Configuration options](#confi The following sections describe several common usage cases. To get started by creating an example pipeline that uses Wave, see [Get started][start]. -[start]: ./get-started.mdx#nextflow +[start]: ./get-started#nextflow ### Access private container repositories diff --git a/docs/provisioning.mdx b/docs/provisioning.md similarity index 100% rename from docs/provisioning.mdx rename to docs/provisioning.md diff --git a/docs/troubleshoot.mdx b/docs/troubleshoot.md similarity index 100% rename from docs/troubleshoot.mdx rename to docs/troubleshoot.md From 481e1b798f91c2f8c6a342756f46076f2271b343 Mon Sep 17 00:00:00 2001 From: Llewellyn vd Berg <113503285+llewellyn-sl@users.noreply.github.com> Date: Wed, 25 Jun 2025 11:50:31 +0200 Subject: [PATCH 4/4] Convert MDX to MD --- docs/{db-migration.mdx => db-migration.md} | 2 +- docs/{wave-lite.mdx => wave-lite.md} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename docs/{db-migration.mdx => db-migration.md} (97%) rename docs/{wave-lite.mdx => wave-lite.md} (100%) diff --git a/docs/db-migration.mdx b/docs/db-migration.md similarity index 97% rename from docs/db-migration.mdx rename to docs/db-migration.md index db74ea0fd..66e05ad04 100644 --- a/docs/db-migration.mdx +++ b/docs/db-migration.md @@ -1,7 +1,7 @@ # Wave Database Migration from SurrealDB to PostgreSQL ## Pre-requisites -- Install [wave-cli] (https://github.com/seqeralabs/wave-cli) +- Install [wave-cli](https://github.com/seqeralabs/wave-cli) - Ensure you have a PostgreSQL database set up and accessible from wave. ## Migration Steps diff --git a/docs/wave-lite.mdx b/docs/wave-lite.md similarity index 100% rename from docs/wave-lite.mdx rename to docs/wave-lite.md