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Align parabricks subworkflow #6876

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famosab
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@famosab famosab commented Oct 28, 2024

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 famosab mentioned this pull request Oct 28, 2024
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@famosab famosab linked an issue Oct 29, 2024 that may be closed by this pull request
new subworkflow: fastq_align_parabricks #6894
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famosab commented Nov 18, 2024

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)

@famosab famosab added help wanted Extra attention is needed gpu module uses GPU labels Nov 18, 2024
maxulysse
maxulysse reviewed Nov 18, 2024
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subworkflows/nf-core/fastq_align_parabricks/main.nf Outdated
Comment on lines 28 to 29
ch_qc_metrics = ch_qc_metrics.mix(PARABRICKS_FQ2BAM.out.qc_metrics)
ch_duplicate_metrics = ch_duplicate_metrics.mix(PARABRICKS_FQ2BAM.out.duplicate_metrics)
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where do you pass this downstream?

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

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new subworkflow: fastq_align_parabricks
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