Nextflow 26.x compat and tabs→spaces in generatemutfasta

[johnoooh]

Fix A

• generatemutfasta tabs→spaces: Converted 3 lines (31-33) in modules/msk/generatemutfasta/main.nf from tab to 4-space indentation in the END_MUTALYZER_CONFIG heredoc. This fixes the YAML runtime error caused by stripIndent() + mixed tab/space indentation.

Fix B

• def keyword for Nextflow 26.x: Added def to 12 local variables across 3 subworkflow helper functions:
• generate_mutated_peptides/main.nf → createNEOSVInput() (3 vars)
• netmhcstabandpan/main.nf → createNETMHCInput() (5 vars)
• phylowgs/main.nf → join_maf_with_cnv() (4 vars)
  This prepares us for nextflow v26

PR checklist

Closes #XXX

• This comment contains a description of changes (with reason).
• 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 fulfill 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

[nikhil]

Variables, tabs and spaces oh my!