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Remove varianble's 'def' from samtool sort 'output_file' - #12582

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Remove varianble's 'def' from samtool sort 'output_file'#12582
bagnacan wants to merge 2 commits into
nf-core:masterfrom
bagnacan:test-samtool-sort

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@bagnacan

@bagnacan bagnacan commented Aug 4, 2026

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This PR removes a variable's def to fix an error encountered while running samtools/sort using Nextflow 24.04.2:

ERROR ~ Module compilation error
- file : /path/to/pipeline/./workflows/../modules/nf-core/samtools/sort/main.nf
- cause: Variable `prefix` already defined in the process scope @ line 36, column 26.
       def output_file = "${prefix}.${extension}"

PR checklist

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

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