Align parabricks subworkflow

[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.
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• Emit the versions.yml file.
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• 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]

Somehow I always get the following error:

│   Nextflow stdout:                                                                                                                                                                                                                        │
│                                                                                                                                                                                                                                           │
│   ERROR ~ Error executing process > 'FASTQ_ALIGN_PARABRICKS:PARABRICKS_APPLYBQSR (test)'                                                                                                                                                  │
│                                                                                                                                                                                                                                           │
│   Caused by:                                                                                                                                                                                                                              │
│     Missing output file(s) `*.bam` expected by process `FASTQ_ALIGN_PARABRICKS:PARABRICKS_APPLYBQSR (test)` (note: input files are not included in the default matching set)    

[maxulysse]

where do you pass this downstream?

[famosab]

I planned to emit it in the end, its not needed for applybqsr though.