Create patches for umi-tools

[MatthiasZepper]

This PR is a hotfix for the 3.11 release candidate to add additional process labels to umi_tools extract (process long) and umi_tools dedup (process high_memory) as a temporary solution to fix errors during pipeline execution until a more appropriate process label has been added to the modules.

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/rnaseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile 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).

[drpatelh]

Thanks! Be awesome if we can just update these on nf-core/modules and re-install here?

[MatthiasZepper]

Sure, but how?

If we change the module, we might want to revert it to process_medium or even add new, more atomic labels? I don't think that this is a good permanent solution, actually...

[drpatelh]

You would create a PR to nf-core/modules with exactly the same changes and then use nf-core modules install to install in the pipeline.

If we change the module, we might want to revert it to process_medium or even add new, more atomic labels? I don't think that this is a good permanent solution, actually...

Are the current label definitions breaking for you on dev? If so, maybe we do need to update. If not, then I think we can leave things as they are and update in a future release. We can suggest to override the defaults with a custom config until we have fixed.

[MatthiasZepper]

Yes, the release candidate version of the pipeline is failing for me with the uppmax profile on a small human sample: umi_tools extract exceeds the runtime and umi_tools dedup the memory limits of process_single as we have defined it in the base.config. This was the reason for my proposal on Slack you have already commented on.

[MatthiasZepper]

Opened a correction PR in the modules repo.

[MatthiasZepper]

Obsolete, as the required changes were directly done to the modules instead of applying patches.