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Closes #9667. Adds hisat3n/build, a tool that builds a 3N-index (containing two hisat2 indexes), from a set of DNA sequences. Tests includes --base-change in nextflow.config ext.args.

  • 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.
  • Broadcast software version numbers to topic: versions - See version_topics
  • 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

@emmcauley emmcauley force-pushed the hisat3n_build branch 2 times, most recently from 54172ba to 70f1bc1 Compare January 15, 2026 15:12

output:
tuple val(meta), path("hisat3n"), emit: index
tuple val("${task.process}"), val('hisat-3n'), eval("hisat-3n --version 2>&1 | grep -o 'version [^ ]*' | cut -d ' ' -f 2"), topic: versions, emit: versions_hisat3n_build
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I suspect the version command could be shortened using sed to do both the grep and the cut

Suggested change
tuple val("${task.process}"), val('hisat-3n'), eval("hisat-3n --version 2>&1 | grep -o 'version [^ ]*' | cut -d ' ' -f 2"), topic: versions, emit: versions_hisat3n_build
tuple val("${task.process}"), val('hisat-3n'), eval("hisat-3n --version 2>&1 | grep -o 'version [^ ]*' | cut -d ' ' -f 2"), topic: versions, emit: versions_hisat3n

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@emmcauley emmcauley Jan 19, 2026

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I'll be adding another module after this called hisat3n_align, which is why I was trying to differentiate -- given that context, does it still make sense to shorten the name?

@emmcauley emmcauley requested a review from SPPearce January 20, 2026 00:59
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new module: hisat3n/build

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