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Add support for fastp length_required #1660

Merged
merged 6 commits into from
Sep 23, 2024
Merged

Add support for fastp length_required #1660

merged 6 commits into from
Sep 23, 2024

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LouisLeNezet
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PR checklist

Add support for the length_required option in fastp.

  • 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/sarek 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).

@LouisLeNezet LouisLeNezet changed the base branch from master to dev September 19, 2024 13:50
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github-actions bot commented Sep 19, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1474c1b

+| ✅ 201 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-19 14:38:48

@nf-core nf-core deleted a comment from github-actions bot Sep 19, 2024
FriederikeHanssen
FriederikeHanssen requested changes Sep 19, 2024
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Can you add this to the changelog and the documentation? Is this the default value for fastp?

@LouisLeNezet
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I will update it as well as the test.yml.
15 is effectively the default value of fastp
https://open.bioqueue.org/home/knowledge/showKnowledge/sig/fastp

@LouisLeNezet
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Should I add some documentation in the output.md ?

@FriederikeHanssen
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I think if it is the default value, than adding that as a note to the params description is fine (so people don't think we changed the default behavior massively). in general, yes adding a note to the fastp section in the output would be good. Something like "contains reads passing the fastp filtering steps for length filtering, ... " etc

maxulysse
maxulysse reviewed Sep 19, 2024
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docs/output.md
- [Strelka](#strelka)
- [Lofreq](#lofreq)
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why changing the order of this?

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In fact I didn't changed this line, this have been done automatically.
But it does reflect that the Strelka paragraph is before Lofreq.

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I think it's a markdown linting thing

FriederikeHanssen
FriederikeHanssen approved these changes Sep 23, 2024
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Nice one!

@LouisLeNezet LouisLeNezet merged commit 163823c into nf-core:dev Sep 23, 2024
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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3 participants
@LouisLeNezet @FriederikeHanssen @maxulysse