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@anoronh4 anoronh4 commented Jul 10, 2023

This is a custom module using awk to split a single fastq or fastq pair into multiple fastqs or fastq pairs, where each comes from a single lane+flowcell source. This is for when the raw data input is merged. This tool uses an awk statement to read the input file and direct the output to different files based on the content of the fastq header. a version of this code is currently implemented in TEMPO

Further described here: nf-core#2836

  • 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.
  • 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:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@anoronh4 anoronh4 marked this pull request as ready for review July 10, 2023 20:38
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