Add index format to samtools view

[fellen31]

Adds an index_format that specifies index generation explicitly (as suggested by @SPPearce), while still allowing for ext.args to contain --write-index (which generates the index with the default samtools index format for the filetype).

Would supersede #4326.

Also:

• fixes stub with unselected.
• Port bam_split_by_region to nf-test.

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

[fellen31]

I believe all remaining lint and pytest-workflow failures are not due to updating this module, but other module updates that I can't adress in this PR.

[SPPearce]

It is trying to lint top-level tools again, rather than the subtool :|
e.g.

Run Linting / nf-core lint modules (graphtyper)

[fellen31]

It is trying to lint top-level tools again, rather than the subtool :| e.g.

Run Linting / nf-core lint modules (graphtyper)

Can we exclude the pytests tests/ directory from the CI? Guessing that is why it's trying to lint top-level?

[fellen31]

It is trying to lint top-level tools again, rather than the subtool :| e.g.

Run Linting / nf-core lint modules (graphtyper)

Making a separate PR: #7482

[fellen31]

Thanks for fixing graphtyper @SPPearce. The remaining pytest is failing because:

Process `test_fastq_create_umi_consensus_fgbio_single_umi:FASTQ_CREATE_UMI_CONSENSUS_FGBIO:FILTERCONSENSUS` declares 5 input channels but 2 were specified
Process `test_fastq_create_umi_consensus_fgbio_duplex_umi:FASTQ_CREATE_UMI_CONSENSUS_FGBIO:CALLDUPLEXCONSENSUS` declares 3 input channels but 1 were specified

This has nothing to do with the changes in this PR, and I don't really understand the subworkflow well enough to fix it. Could we ignore this?

[SPPearce]

Yeah, that subworkflow is broken already by the looks of it at the moment.

[SPPearce]

Looks like I broke it when I updated the fgbio modules, but the subworkflow tests didn't run: #5624