Replace alevinqc with qcatch for simpleaf QC

[an-altosian]

• Update simpleaf modules to 0.19.5
• Add qcatch module from local modules repo
• Add qcatch chemistry mappings to protocols.json
• Update simpleaf subworkflow to use QCATCH
• Add skip_qcatch parameter for optional QC
• Remove alevinqc module and bin/alevin_qc.r
• Update test config and snapshots

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!
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• 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).

[an-altosian]

I am almost done with this PR, just need to grab a dataset to test. This can be a breaking change because I replaced alevinqc with qcatch

[nf-core-bot]

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[fmalmeida]

Hi there,

Thanks for the PR.

Do we have an issue that was tracking the request?

And the testing dataset can be the same that was being used for alevin, no?

[fmalmeida]

Adding some ideas :)

[fmalmeida]

These env variables maybe can be set directly in the nextflow.config as env there so all python modules already use it by default.

Instead of adding in each, no?

[an-altosian]

Thank you @fmalmeida! I will address your comments. BTW, I also mde a PR for nf-core qcatch module nf-core/modules#10032 . I will update there as well.

For the test dataset, as qcatch does cell calling internally (we reverse engineered cellranger's cell calling algorithm) and exports a filtered count matrix, it only works on real datasets. I tried to use the test dataset we have, but it gave me error saying insufficient data for cell calling. Therefore, I end up with doing the same thing we did for cellblender.

In the nf-core/module, I have tests using real data we used in the qcatch github repo. As we will pull the module directly from nf-core/modules, I think we are good even if we don't have tests for qcatch here.

[an-altosian]

All comments resolved. I will find a dataset to test.

[an-altosian]

The failing test seems to be related to STAR.

[an-altosian]

Tested. Ready to merge

[fmalmeida]

Thank you @fmalmeida! I will address your comments. BTW, I also mde a PR for nf-core qcatch module nf-core/modules#10032 . I will update there as well.

For the test dataset, as qcatch does cell calling internally (we reverse engineered cellranger's cell calling algorithm) and exports a filtered count matrix, it only works on real datasets. I tried to use the test dataset we have, but it gave me error saying insufficient data for cell calling. Therefore, I end up with doing the same thing we did for cellblender.

In the nf-core/module, I have tests using real data we used in the qcatch github repo. As we will pull the module directly from nf-core/modules, I think we are good even if we don't have tests for qcatch here.

Maybe we should focus on merging the nf-core/modules first, because there we will have automated testing for the module. So we then bring it here to this PR ... this would help with the testings, since the pipeline small test cannot be used.

Any other comments @grst and @nictru ?