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Lint fastqs before and during preprocessing #7123

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merged 10 commits into from
Dec 2, 2024
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Adds a lint check at every step during preprocessing. FQ_LINT will fail, and does not return fastqs, so I just do a dummy join to make sure things don't go to other processes at

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.
  • Emit the versions.yml file.
  • Follow the naming conventions.
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  • 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

@pinin4fjords pinin4fjords added this pull request to the merge queue Dec 2, 2024
Merged via the queue into master with commit 34774b3 Dec 2, 2024
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@pinin4fjords pinin4fjords deleted the fq_preprocess_lint branch December 2, 2024 15:57
LouisLeNezet pushed a commit to LouisLeNezet/modules that referenced this pull request Dec 4, 2024
* Lint fastqs before and during preprocessing

* Add lint_log to snaps

* put back file removed in error

* Update snap

* Fix tests

* Linting snapshots to md5

* Update subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf

Co-authored-by: Maxime U Garcia <[email protected]>

* Update swf meta.yml

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Co-authored-by: Maxime U Garcia <[email protected]>
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3 participants