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/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/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 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