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Remove trimming #208

Merged
merged 5 commits into from
Jul 24, 2024
Merged

Remove trimming #208

merged 5 commits into from
Jul 24, 2024

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nschcolnicov
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This PR fixes this issue: #207

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/demultiplex 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>).
  • 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).

@nschcolnicov nschcolnicov requested a review from a team as a code owner July 23, 2024 19:17
@nschcolnicov nschcolnicov requested review from kobelavaerts and removed request for a team July 23, 2024 19:17
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github-actions bot commented Jul 23, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 885e867

+| ✅ 182 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-24 11:34:42

grst
grst approved these changes Jul 24, 2024
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LGTM, just suggesting to make it explicit that this is for Illumina samplesheets

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grst commented Jul 24, 2024

(Apart from that I think trimming should be better documented, as mentioned in #207, but that can be a separate PR)

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(Apart from that I think trimming should be better documented, as mentioned in #207, but that can be a separate PR)

Sounds good, I created #209 for this. I wasn't sure exactly what to write and where to place it and I want it to apply these changes as soon as possible.

fmalmeida
fmalmeida reviewed Jul 24, 2024
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otherwise, looks good.

nextflow.config
@@ -15,6 +15,7 @@ params {

// Options: trimming
trim_fastq = true // [true, false]
remove_adapter = true // [true, false]
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When I first read this parameter, I interpret as trimming it, like removing from the sequence.

Reading the rest I know it refers to removing from the samplesheet to avoid trimmimg.

But, I just wanted to bring this up, as maybe the parameter can be more explicit to avoid such confusion.

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Thank you for your feedback. I understand the possible confusion about the parameter name. Since this parameter follows 10x's recommended method and is usually left as default, most users won't need to change it. If users do want to change it, they will likely have to read the documentation for details, so I don't think it should be too much of an issue.

@nschcolnicov nschcolnicov merged commit 4f6a841 into nf-core:dev Jul 24, 2024
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@apeltzer apeltzer mentioned this pull request Aug 12, 2024
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@fmalmeida fmalmeida fmalmeida left review comments

@grst grst grst approved these changes

@kobelavaerts kobelavaerts Awaiting requested review from kobelavaerts kobelavaerts is a code owner automatically assigned from nf-core/demultiplex

@atrigila atrigila Awaiting requested review from atrigila

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@nschcolnicov @grst @fmalmeida