Change simpleaf protocol name from 10xv4 to 10xv4-3p

[milos7250]

At this moment, running the pipeline on samples with 10XV4 protocol and simpleaf aligner fails. As can be seen in the list of supported chemistries in simpleaf, the chemistry 10xv4 does not exist, they only have 10xv4-3p available. This issue was not flagged in tests, as the test dataset is only using 10xv2 protocol.

This PR only changes the protocol name for this particular chemistry, but perhaps the whole list should be changed to more closely follow the list of available chemistries of simpleaf?

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[milos7250]

I believe I have now included everything that is mentioned in the contributing guidelines, except writing a new test for this fix. This would require adding more data to the test branch and adding more tests.

I cancelled the tests for the previous commit, as it felt wasteful to run the same tests after only updating the changelog.

[grst]

Hi @milos7250,

thanks a lot for fixing that! Please make always sure to use the dev branch to start off your changes and make PRs only against the dev branch. The master branch is only for releases.

I cancelled the tests for the previous commit, as it felt wasteful to run the same tests after only updating the changelog.

Also please don't do this. Github actions is setup as a mandatory check in this repository, so if it does not run through on the latest commit, merging is blocked.

Would you mind fixing the merge conflicts and then I take another look?

[milos7250]

Hi @grst,

sorry for the confusion with the branches, I was looking at https://github.com/nf-core/scrnaseq/blob/master/.github/CONTRIBUTING.md#patch when I was deciding which branch to create the PR against. Is that information incorrect? Do you prefer bug fix PRs to be created against dev?

I will have a look at the conflicts in a minute.

[grst]

ah, I was already wondering why the "branch protection" github action didn't flag this, but you are right, "patches" can be merged directly in the main branch.

I would, however, prefer to bundle this in the dev branch and maybe fix 1-2 more things before making a patch release. I usually try to keep the dev branch in a state that always allows me to make a release if necessary.

[milos7250]

That's the dev branch now merged into here @grst.

[grst]

Thanks @milos7250!