8000 Fix CAT_FASTQ handling for long reads and hybrid assembly modes by Daniel-VM · Pull Request #248 · nf-core/bacass · GitHub
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Fix CAT_FASTQ handling for long reads and hybrid assembly modes #248

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Merged
merged 8 commits into from
Jul 11, 2025
Merged

Fix CAT_FASTQ handling for long reads and hybrid assembly modes #248

merged 8 commits into from
Jul 11, 2025

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Daniel-VM
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@Daniel-VM Daniel-VM commented Jul 1, 2025 •
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PR checklist

  • 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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/bacass branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

PR description

Extends reads concatenation functionality to work properly in long and hybrid assembly modes, not just short reads mode. Major changes:

  • Add separate CAT_FASTQ processes for short and long reads
  • Set single_end: true for long reads to prevent paired-end output
  • Use concatenated channels consistently in downstream QC processes
  • Add conditional logic based on assembly_type parameter

Close #230

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nf-core-bot commented Jul 1, 2025 •
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@Daniel-VM Daniel-VM marked this pull request as ready for review July 1, 2025 12:28
d4straub
d4straub approved these changes Jul 7, 2025
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I think that looks fine. As detailed below I would avoid having twice the same flatten call in branching and rather do that earlier.

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Daniel-VM commented Jul 10, 2025 •
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[update] @d4straub , fixed cat_fastq performance when runing in assembly-hybrid mode. In addition I have updated the nf-test of this module. (git ci tests ran twice without errors)

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d4straub commented Jul 11, 2025 •
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Awesome, looks good. I had a look at the code again and all seemed fine to me. Good to merge I think!

@Daniel-VM Daniel-VM merged commit 61d62d6 into nf-core:dev Jul 11, 2025
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