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Development Environment

A development environment for running the pipeline and executing tests can be created with mamba.

After installing mamba, the development environment can be created and activated with:

mamba env create --file environment-dev.yml
mamba activate longplex-nf-dev

The integration tests can be run with:

pytest --tag integration

Before Release

Before creating a new release, confirm wf/entrypoint has been updated to pass any newly added parameters to the underlying workflow.

Creating a New Release

Update the Version

In your local copy of the repository checkout the commit you wish to use for the next release.

Typically, this will be the latest commit on main.

git checkout main
git pull

Update the version stored in the version file. See sematic versioning for guidance on picking an appropriate version number.

Create a commit with the updated version file where #.#.# is the newly picked semantic version.

git add version
git commit -m "chore: update to version #.#.#"

Register the Workflow

Login to latch.

latch login

If this process generates a warning that the installed version of latch should be upgraded, then you should update the version of latch specified in environment-dev.yml and the latch config. If you update those files be sure to commit the changes.

git add environment-dev.yml .latch/config
git commit -m "chore: bump latch version"

Register the workflow.

latch register .

Warning

Do not run latch register . -nf-script main.nf --nf-execution-profile docker as this will overwrite the custom wf/entrypoint.py file.

Commit and Push Release to GitHub

git add .latch/Dockerfile
git commit -m "chore: update Latch resource files"

Tag the commit with the version for traceability:

git tag #.#.#

Push the commits and tag up to GitHub.

git push --follow-tags

Promote the Registered Workflow on Latch

  1. On Latch, select the "seqWell LongPlex Demux" workflow.
  2. Select the "Development" tab.
  3. Expand the dropdown for the appropriate version.
  4. Create an alias for the version, v#.#.#.
  5. Fill in the "Version Notes" with a list of changes made since the previous release.
  6. Select "Release".
  7. Select "Make Public".
  8. Select "Confirm".

Switch the Main Branch version to a Dev Version

Follow the instructions under "Update the Version" but specify a dev version, #.#.#-dev. Push the change to GitHub.