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add bbmap clumpify #52

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erkutilaslan
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added clumpify module to the pipeline.
not sure if any of its outputs goes into multiqc (other than version).

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

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github-actions bot commented Oct 29, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b0e2558

+| ✅ 188 tests passed       |+
!| ❗  21 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
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✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-29 10:46:47

MatthiasZepper
MatthiasZepper requested changes Oct 29, 2024
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Thank you for the contribution and working on this task!

Unfortunately, I am missing any configuration for this module. This is highly relevant for two reasons:

1.) The publishDir directive: Initially, we had decided that Seqinspector would only inspect reads, but not alter them in any way (e.g. perform adapter-trimming) However, I agree that it is convenient to be able to perform some basic error correction and optimization in the process as well. Therefore, I support the addition of such a step, but you need to publish the resulting files so they are available later in the output directory.
2.) Currently, there are no arguments defined for the tool. Particularly for tools from the BBMap Suite, the sheer amount of settings can be overwhelming, but the arguments are also very useful for advanced customization. Please read through the description of arguments and propose some decent defaults. Hint: Consider predominantly k, subs, lowcomplexity and reorder. If you would like to enable deduplication (dedupe=t) as well, choices for dupedist, scanlimit, spantiles, adjacent and optical must be made.

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@MatthiasZepper MatthiasZepper MatthiasZepper requested changes

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@erkutilaslan @MatthiasZepper