Adding CircularMapper as module to nf-core

[shyama-mama]

PR checklist

Opened as part of https://github.com/nf-core/eager/issues/1033 Adding CircularMapper to nf-core modules for lifter over of eager functionality from DSL1 to DSL2

• [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

[shyama-mama]

I've fixed the issues with prettier and formatting. But I'm not sure what is happening with pytests failing. The docker version I run locally finishes successfully.

[SPPearce]

I've fixed the issues with prettier and formatting. But I'm not sure what is happening with pytests failing. The docker version I run locally finishes successfully.

Conda often gives different md5sums for bam files whenever they have been through bwa or samtools, as the header of the bam file contains paths to the tools which are slightly different between docker/singularity and conda. You can avoid this by not testing the md5sums for the bam files.

[shyama-mama]

@SPPearce Sorry! I'm struggling to decrypt these errors again, again the pytest on docker works fine locally. Not sure why it is complaining about some bowtie2 file not being found.

[SPPearce]

@SPPearce Sorry! I'm struggling to decrypt these errors again, again the pytest on docker works fine locally. Not sure why it is complaining about some bowtie2 file not being found.

Those are weird errors that I don't understand, but seem to be related to the pytest tests/ files not being present in the git repo. I'm rerunning the tests to see if that helps magically. We are in the process of migrating from pytest to nf-test, with nf-test now being the standard, so might be something to do with that.

[shyama-mama]

If everything looks good to you @SPPearce I'm happy for this to be merged.

[SPPearce]

Hi @jbv2 , it looks like the module has been added in #5326, so I'm going to close this one.