Skip to content

Commit

Permalink
Fix Tower doc links, fix typos (#3647) [ci skip]
Browse files Browse the repository at this point in the history
Signed-off-by: Llewellyn vd Berg <113503285+llewellyn-sl@users.noreply.github.com>
  • Loading branch information
llewellyn-sl committed Feb 15, 2023
1 parent 0a355ac commit 1278e1a
Showing 1 changed file with 15 additions and 16 deletions.
31 changes: 15 additions & 16 deletions docs/wave.rst
Expand Up @@ -48,9 +48,9 @@ Authenticate private repositories
---------------------------------

Wave allows the use of private repositories in your Nextflow pipelines. The repository access keys need to be provided
via the `Nextflow Tower credentials <https://help.tower.nf/22.2/credentials/overview/>`_ manager feature.
via the `Nextflow Tower credentials <https://help.tower.nf/latest/credentials/registry_credentials/>`_ manager feature.

Once the credentials have been created, you only need to specify your `Tower account access token <https://help.tower.nf/22.2/api/overview/#authentication>`_
Once the credentials have been created, you only need to specify your `Tower account access token <https://help.tower.nf/latest/api/overview/#authentication>`_
in your pipeline configuration file. If the credentials were created in a Tower organization workspace, specify the workspace ID
as well in the config file as shown below::

Expand Down Expand Up @@ -83,16 +83,16 @@ The above line instructs Wave to give the module Dockerfile priority over proces
Wave currently does not support ``ADD``, ``COPY`` and other Dockerfile commands that access files in the host
file system.

Build Conda based containers
Build Conda-based containers
----------------------------

Wave allows the provisioning of containers based on the :ref:`process-conda` directive used by the processes in your
pipeline. This is a quick alternative to building Conda packages in the local computer. Moreoever, this enables the use of
pipeline. This is a quick alternative to building Conda packages in the local computer. Moreover, this enables the use of
Conda packages in your pipeline when deploying it in cloud-native platforms such as AWS Batch and Kubernetes,
which do not allow the (easy) use of the Conda package manager.

Having Wave enabled in your pipeline, there's nothing else to do other than define the ``conda`` requirements in
the pipeline processes provided the same process does not also specify a ``container`` directive or a Dockerfile.
With Wave enabled in your pipeline, you need only to define the ``conda`` requirements in
the pipeline processes, provided the same process does not also specify a ``container`` directive or a Dockerfile.

In the latter case, add the following setting to your pipeline configuration::

Expand All @@ -105,19 +105,18 @@ Push to a private repository
----------------------------

Containers built by Wave are uploaded to the Wave default repository hosted on AWS ECR with name
``195996028523.dkr.ecr.eu-west-1.amazonaws.com/wave/build``. The images in this repository are automatically deleted
after 1 week from the date of their push.
``195996028523.dkr.ecr.eu-west-1.amazonaws.com/wave/build``. The images in this repository are automatically deleted 1 week after the date of their push.

If you want to store Wave containers in your own container repository use the following settings in
If you want to store Wave containers in your own container repository, use the following settings in
the Nextflow configuration file::

wave.build.repository = 'example.com/your/build-repo'
wave.build.cacheRepository = 'example.com/your/cache-repo'

The first repository is used to store the built container images. The second one is used to store the individual image layers for caching purposes.

The repository access keys need to be specified using the Tower credentials manager as specified in the
`Authenticate private repositories`_ section.
The repository access keys need to be specified using the Tower credentials manager, per the
`Authenticate private repositories`_ section above.


Advanced settings
Expand All @@ -130,11 +129,11 @@ Name Description
============================================== =================
wave.enabled Enable/disable the execution of Wave containers
wave.endpoint The Wave service endpoint (default: ``https://wave.seqera.io``)
wave.build.repository The container repository where image built by Wave needs to be uploaded (note: the corresponding credentials need to be provided in your Nextflow Tower account).
wave.build.cacheRepository The container repository used to cache image layers build by the Wave service (note: the corresponding credentials need to be provided in your Nextflow Tower account).
wave.conda.mambaImage The Mamba container image is used to build Conda based container. This is expected to be `micromamba-docker <https://github.com/mamba-org/micromamba-docker>`_ image.
wave.conda.commands One or more commands to be added to the Dockerfile used by build a Conda based image.
wave.strategy The strategy to be used when resolving ambiguous Wave container requirement (default: ``'container,dockerfile,conda'``)
wave.build.repository The container repository where images built by Wave need to be uploaded (note: the corresponding credentials need to be provided in your Nextflow Tower account).
wave.build.cacheRepository The container repository used to cache image layers built by the Wave service (note: the corresponding credentials need to be provided in your Nextflow Tower account).
wave.conda.mambaImage The Mamba container image is used to build the Conda-based container. This is expected to be the `micromamba-docker <https://github.com/mamba-org/micromamba-docker>`_ image.
wave.conda.commands One or more commands to be added to the Dockerfile used to build a Conda-based image.
wave.strategy The strategy to be used when resolving ambiguous Wave container requirements (default: ``'container,dockerfile,conda'``)
============================================== =================

More examples
Expand Down

0 comments on commit 1278e1a

Please sign in to comment.