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Update presto filterseq module#12205

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Vivian0105 wants to merge 4 commits into
nf-core:masterfrom
Vivian0105:update_presto_filterseq
Open

Update presto filterseq module#12205
Vivian0105 wants to merge 4 commits into
nf-core:masterfrom
Vivian0105:update_presto_filterseq

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@Vivian0105

@Vivian0105 Vivian0105 commented Jun 30, 2026

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  1. Update to the latest presto version.
  2. Read and write fastq.gz file directly which is the new feature of presto.
  3. Use topic channel for versions.

Opened issue: #12192

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

@Vivian0105 Vivian0105 requested a review from ggabernet June 30, 2026 15:12
Comment thread modules/nf-core/presto/filterseq/main.nf Outdated
Comment thread modules/nf-core/presto/filterseq/main.nf Outdated
Vivian0105 and others added 2 commits June 30, 2026 13:10
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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2 participants