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Proposed fix for MirTrace uses untrimmed fastq input #242 #243

Merged
merged 2 commits into from
May 8, 2023
Merged

Proposed fix for MirTrace uses untrimmed fastq input #242 #243

merged 2 commits into from
May 8, 2023

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apeltzer
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@apeltzer apeltzer commented May 8, 2023

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/smrnaseq 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).

@apeltzer apeltzer requested review from robsyme and maxulysse May 8, 2023 13:03
apeltzer
apeltzer commented May 8, 2023
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subworkflows/local/fastqc_fastp.nf
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@maxulysse maxulysse mentioned this pull request May 8, 2023
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github-actions bot commented May 8, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 54554a3

+| ✅ 158 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '2.2.1'
  • 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 README.md: update the following command to include all required parameters for a minimal example

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-08 13:45:59

robsyme
robsyme approved these changes May 8, 2023
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Great. Thanks Alex!

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apeltzer commented May 8, 2023

Thank you for helping here :)

@apeltzer apeltzer merged commit 0a8ffd6 into dev May 8, 2023
@maxulysse maxulysse deleted the fix-mirtrace-inputs branch May 8, 2023 14:47
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@maxulysse maxulysse maxulysse approved these changes

@robsyme robsyme robsyme approved these changes

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@apeltzer @robsyme @maxulysse