MuTect2 Module

[rnaidu]

PR checklist

• Module created for MuTect2 variant caller. MSK-modules version is being created for MuTect2 since nf-core MuTect module includes two mandatory file parameters (panel of normals and germline resources) which are not needed in the base command reflected in this module. Please refer to nf-core MuTect2 module docs for more info: https://nf-co.re/modules/gatk4_mutect2
• Check to see if a nf-core module, or subworkflow is available and usable for your pipeline.
• Feature branch is named feature/<module_name> for modules, or feature/<subworkflow_name> for subworkflows. For modules, if there is a subcommand use: feature/<module_name>/<module_subcommand>.
• 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.
• Use nf-core data if possible for nf-tests. If not, use or add test data to mskcc-omics-workflows/test-datasets, following the repository guidelines, for nf-tests. Finally, if neither option is feasible, only add a stub nf-test.
• 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 Jfrog 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 --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile docker
    • nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile singularity
    • nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile conda

[buehlere]

The testing and linting aren't running properly for this modules. I think it might be because you're missing some testing files.

[buehlere]

I think you're missing the tag.yml and main.nf.test.snap files. You might want to double check some other parts of the nf-test. This might be why the testing and linting aren't running properly?

[johnoooh]

Might be good to add in an arg here so we can add java options. In tempo we set the Xmx for example so it may be good to add a ${jvmarg} here or something. This is how it looks in our Tempo Module.