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Fix stub run trimmomatic #7160

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Fix stub run trimmomatic #7160

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@kiei-rz kiei-rz commented Dec 4, 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

SPPearce
SPPearce approved these changes Dec 5, 2024
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modules/nf-core/trimmomatic/main.nf
@@ -50,12 +50,12 @@ process TRIMMOMATIC {
def prefix = task.ext.prefix ?: "${meta.id}"

if (meta.single_end) {
output_command = "echo '' | gzip > ${prefix}.SE.paired.trim.fastq.gz"
output_command = "echo '' | gzip > ${prefix}.SE.paired.trim.fastq.gz\n"
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@SPPearce SPPearce Dec 5, 2024 •
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Not sure it needs the explicit line break at the last entry does it (same with the paired end underneath)?

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@SPPearce SPPearce SPPearce approved these changes

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@kiei-rz @SPPearce