Add module muse/call

[famosab]

PR checklist

Closes #5621

• 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 module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• 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:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

The Docker image still needs to be pushed to the nf-core registry, then I can update the paths accordingly. Also relates to #5629

[SPPearce]

Could this tool be added to BioConda? Then the other containers would be generated automatically

[famosab]

I opened a PR: bioconda/bioconda-recipes#47957

If that works, I will change the files in this PR accordingly

[SPPearce]

A few comments.

[SPPearce]

Does the tool use the indexes of the sorted bam files if they are present? If so, they should be passed in too.

[famosab]

i am not sure, from the tool description it seems that it takes care of this inside of the tool (tabix is one of the dependencies)

[SPPearce]

Can you ask the authors please? As often the tools assume that the index is next to the bam file, which will generally work fine with symlinks on a HPC system but isn't true for cloud execution.

[SPPearce]

An indexed file? Does that mean it wants the index to be present alongside?

[famosab]

I just copied that from the module description but to me it seems that is also happy with just the fasta file

[SPPearce]

It would be good to check about the indexes (bam and fasta), but otherwise I'm happy.

[SPPearce]

Can you ask the authors please? As often the tools assume that the index is next to the bam file, which will generally work fine with symlinks on a HPC system but isn't true for cloud execution.

[famosab]

I asked here: wwylab/MuSE#31
Will wait for their reply and merge afterwards :)