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Fix paired end sample handling #439

Merged
merged 1 commit into from
Sep 25, 2024
Merged

Fix paired end sample handling #439

merged 1 commit into from
Sep 25, 2024

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nschcolnicov
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Addresses #415

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 (nf-test test main.nf.test -profile test,docker).
  • 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).

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github-actions bot commented Sep 24, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7c1106a

+| ✅ 223 tests passed       |+
#| ❔   1 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:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-24 21:18:00

@nschcolnicov nschcolnicov mentioned this pull request Sep 24, 2024
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@apeltzer apeltzer mentioned this pull request Sep 25, 2024
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@nschcolnicov
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Tests are passing in their current state, but we need to wait until nf-core/test-datasets#1337 is merged, and then re run the tests before merging this PR

@apeltzer apeltzer marked this pull request as ready for review September 25, 2024 17:52
@nschcolnicov nschcolnicov merged commit d86d425 into nf-core:dev Sep 25, 2024
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@atrigila atrigila atrigila approved these changes

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@nschcolnicov @atrigila