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Add cutadapt #95

Merged
merged 8 commits into from
Dec 12, 2023
Merged

Add cutadapt #95

merged 8 commits into from
Dec 12, 2023

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LaurenceKuhl
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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/crisprseq 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 29, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 62c0525

+| ✅ 158 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowCrisprseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-30 09:50:01

@LaurenceKuhl
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@nf-core-bot fix linting

mirpedrol
mirpedrol reviewed Dec 7, 2023
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docs/output/screening.md Outdated

</details>

[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
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This description should be updated :)

nextflow_schema.json Outdated
@@ -183,6 +183,10 @@
"type": "string",
"description": "sgRNA library annotation for crisprcleanR"
},
"cutadapt": {
"type": "string",
"description": "cutadapt adapter"
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Can we add that this is used for the screening workflow?

mirpedrol
mirpedrol approved these changes Dec 7, 2023
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LGTM :)

@LaurenceKuhl LaurenceKuhl merged commit e0fd8d3 into nf-core:dev Dec 12, 2023
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@mirpedrol mirpedrol mirpedrol approved these changes

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@LaurenceKuhl @mirpedrol @nf-core-bot