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Merged
merged 3 commits into from
Mar 31, 2025
Merged

Add subworkflow mapping statistics #146

merged 3 commits into from
Mar 31, 2025

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sainsachiko
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@sainsachiko sainsachiko commented Mar 31, 2025

Add subworkflow MAPPING_STATISTICS #129 with:

  • seqtk comp
  • seqtk parse

Note: This subworkflow processes the output FASTA file from vcf2pseudogenome.py. However, this module has not yet been integrated into the main workflow. Therefore, mapping_statistics has been tested using independent data with a separate input channel.

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/bactmap branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • 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).

@sainsachiko sainsachiko requested a review from avantonder March 31, 2025 17:24
@sainsachiko sainsachiko changed the title Dev Add subworkflow mapping statistics Mar 31, 2025
@avantonder avantonder merged commit 9099bc7 into nf-core:dev Mar 31, 2025
4 of 6 checks passed
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2 participants