Lint + code polish modules for sarek

[maxulysse]

I ran this on all sarek modules:

nextflow lint -format -sort-declarations -spaces 4 -harshil-alignment ...

(and fixed the issues)

Split in:

• cnvkit: nextflow lint + minor polish + update of cnvkit/batch #8898
• fix gatkspark/applybqsr #8900
• lint | format | fix | polish on all gatk4 #8901
• split out from #8901 #8905
• lint + code polish ascat #8915
• lint + code polish bcftools/annotate #8916

Reducing scope:

• lint + code polish controlfreec #8917 -> Nextflow Language Server Compliance for Freec Modules #9017
• lint + code polish fgbio/fastqtobam #8919
• lint + code polish goleft/indexcov #8920
• lint + code polish lofreq/callparallel #8921
• lint + code polish ngscheckmate/ncm #8922
• lint + code polish sentieon #8923
• lint + code polish unzip #8924

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

[edmundmiller]

Is the plan to get all of the tests to pass?

[maxulysse]

Is the plan to get all of the tests to pass?

yes, but mainly more by splitting up this PR.
This one is more my checklist

[SPPearce]

@maxulysse , can we close this now?