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Fix: Missing import statements on error messages(#1566) #1712

Merged
merged 5 commits into from
Oct 30, 2024
Merged

Fix: Missing import statements on error messages(#1566) #1712

merged 5 commits into from
Oct 30, 2024

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pharmlovex
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@pharmlovex pharmlovex commented Oct 29, 2024 •
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Fix: Missing import statements on error messages when starting without samplesheet (#1566).

Removed the Nexflow (library) called within the groovy function retrieveInput().

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/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).

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github-actions bot commented Oct 29, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e6a6db8

+| ✅ 215 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   4 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!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-30 07:50:19

maxulysse
maxulysse reviewed Oct 30, 2024
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CHANGELOG.md Outdated
@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Fixed

- [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet
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Can you please put this line at the end on the section?

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I have re-ordered the changelog accordingly.
Thanks.

@pharmlovex pharmlovex merged commit 8ea4af9 into nf-core:dev Oct 30, 2024
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@pharmlovex pharmlovex mentioned this pull request Oct 30, 2024
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@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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

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@pharmlovex @maxulysse @FriederikeHanssen