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Add skip_clipping parameter to skip fastp or adapterremoval #361

Merged
merged 8 commits into from
Dec 16, 2022
Merged

Add skip_clipping parameter to skip fastp or adapterremoval #361

merged 8 commits into from
Dec 16, 2022

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prototaxites
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Adds a parameter to skip read QC using either fastp or adapterremoval, to allow the user to jump in straight to assembly if they have pre-processed reads. Also adds a check so that if clipping is skipped, keep_phix is true, and no host fasta or genome is specified, FASTQC_TRIMMED does not run - have also fixed the multiqc call so it can run in this case.

I've added a new test profile (test_no_clipping.config), and have tested all combinations of skip_clipping, keep_phix and host_fasta. The other tests (test.config and test_host_rm.config) still operate as they should.

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/mag 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 --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 Nov 30, 2022 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 53c9844

+| ✅ 148 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌   7 tests failed       |-

❌ Test failures:

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.1
  • Run at 2022-12-15 11:19:49

@jfy133 jfy133 self-requested a review December 1, 2022 08:30
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jfy133 commented Dec 1, 2022

@nf-core-bot fix linting

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jfy133 approved these changes Dec 1, 2022
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Overall looks OK to me (one question about FASTQC_TRIMMEd but that's it)

workflows/mag.nf Show resolved Hide resolved
@prototaxites
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@d4straub This one is now also failing because of linting (I wasn't sure what the etiquette around merging was!) - would it be possible to merge it also?

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After approval, the PR author may merge the PR, sometimes some comments are still open but we trust that this is fixed.
I'll merge it.

@d4straub d4straub merged commit c3a0ef3 into nf-core:dev Dec 16, 2022
@prototaxites prototaxites deleted the skip_qc branch December 16, 2022 10:38
@jfy133 jfy133 mentioned this pull request Feb 27, 2023
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@d4straub d4straub d4straub left review comments

@jfy133 jfy133 jfy133 approved these changes

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