Module: ichorcna/run updated to v0.5.0

[adamrtalbot]

Changes:

• ichorcna no longer has a CLI, so it has been updated to use native R
• Some additional parameters have been added
• Requires scStates option in nextflow.config or it crashes

PR checklist

• [x] This comment contains a description of changes (with reason).
• [x] If you've fixed a bug or added code that should be tested, add tests!
• [x] If you've added a new tool - have you followed the module conventions in the contribution docs
• [x] If necessary, include test data in your PR.
• [x] Remove all TODO statements.
• [x] Emit the versions.yml file.
• [x] Follow the naming conventions.
• [x] Follow the parameters requirements.
• [x] Follow the input/output options guidelines.
• [x] Add a resource label
• [x] Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • [x] PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • [ ] PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • [ ] PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

[adamrtalbot]

@nf-core-bot fix linting

[SPPearce]

Looks generally good, few minor points. Is the meta.yml not updated? Presumably that still points at the old broad institute github link.

[adamrtalbot]

@nf-core-bot fix linting

[github-actions[bot]]

Nothing for me to do here! :shrug: This is probably because the linting errors come from nf-core lint and have to be fixed manually (or with nf-core lint --fix).

[adamrtalbot]

@nf-core-bot fix linting

[SPPearce]

Hey @adamrtalbot , shall we get this finished off and merged in?

[adamrtalbot]

Hey @adamrtalbot , shall we get this finished off and merged in?

What do we need to do? I need a ✅ review to get this merged.

[SPPearce]

I have a half-done conversion to nf-test actually

[SPPearce]

Superceded by #6079 as I couldn't edit Adam's branch.