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New module bwafastalign-index#11843

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new-module-bwa-fastalign-index
Open

New module bwafastalign-index#11843
peterpru wants to merge 22 commits into
masterfrom
new-module-bwa-fastalign-index

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@peterpru peterpru commented Jun 3, 2026

This PR adds the bwa-fastalign index subtool, needed for bwa-fastalign mem. See issue #11835

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.
  • 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

@peterpru peterpru self-assigned this Jun 3, 2026
@github-actions github-actions Bot added the size/m label Jun 3, 2026
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peterpru commented Jun 3, 2026

Need correct containers/conda and test snapshots.

@ramprasadn
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@nf-core-bot fix linting

@ramprasadn
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@nf-core-bot fix linting

@peterpru peterpru enabled auto-merge June 5, 2026 11:10
Comment thread modules/nf-core/bwafastalign/index/tests/nextflow.config
Comment thread modules/nf-core/bwafastalign/index/environment.yml
Comment thread modules/nf-core/bwafastalign/index/main.nf
@ramprasadn ramprasadn requested a review from maxulysse June 8, 2026 11:30
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4 participants