port parabricks/mutectcaller to nf-test

[famosab]

PR checklist

Closes #XXX

• 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

[famosab]

PON test does not work because:
// // PON test not passing because the tool expects all chromosomes in the PON file to
// // be present in the reference genome.

Tumor-Normal tests do not work because:
// // tumor-normal calling not passing because of issue with readgroups in the test files
// // [PB Error][src/readers.cpp:1314] ID simulation01 maps to tm_simulation01, but PU is nm_simulation01 (different platform), exiting.

[famosab]

Intervals test fails with

│     /usr/local/parabricks/binaries/bin/mutect genome.fasta test2.paired_end.recalibrated.sorted.bam 1 -o test.vcf.gz -tumorsample tumor -nt 5 -L multi_intervals.bed -max-mnp-distance 1 --low-memory                                                                                                                       │
│     Exit with error: 1                                                                                                                                                                                                                                                                                                      │
│     For technical support visit https://docs.nvidia.com/clara/index.html#parabricks                                                                                                                                                                                                                                         │
│     Exiting...                                                                                                                                                                                                                                                                                                              │
│     Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation    

[SPPearce]

Looks good to me. Can you just link to an issue to help track the stageInMode please, and make sure there is an issue to fix the tests for tumour/normal mode.

[famosab]

@SPPearce Do you think its fine to leave in the outcommented tests? I left them for later reference or that someone whos a bit more skilled might be able to fix them - but the general testing works so I did not bother to spend more time on this.

[famosab]

Opened an issue in this repo, will link if I find any description at the parabricks website: #7226

[SPPearce]

@SPPearce Do you think its fine to leave in the outcommented tests? I left them for later reference or that someone whos a bit more skilled might be able to fix them - but the general testing works so I did not bother to spend more time on this.

Fine by me to leave them.