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print warnings instead of erroring #1673

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Merged
maxulysse merged 7 commits into from
Oct 3, 2024
Merged

print warnings instead of erroring #1673

maxulysse merged 7 commits into from
Oct 3, 2024

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@maxulysse maxulysse commented Oct 3, 2024 •
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fix #1672

  • works well with local/s3 file

  • stream fails with http file (which is what was silent before), but we still get the first line correctly

  • now print a warning message if we cannot assess flowcell id from the fastq file

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 3, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 70b10c3

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

❗ 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 2024-10-03 09:33:41

FriederikeHanssen
FriederikeHanssen reviewed Oct 3, 2024
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FriederikeHanssen
FriederikeHanssen reviewed Oct 3, 2024
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FriederikeHanssen
FriederikeHanssen previously approved these changes Oct 3, 2024
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sorry misread, the two error codes are thrown unrelated from each other

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FriederikeHanssen commented Oct 3, 2024

needs a changelog update

@maxulysse maxulysse merged commit 2be5d14 into nf-core:dev Oct 3, 2024
@maxulysse maxulysse mentioned this pull request Oct 14, 2024
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@maxulysse maxulysse deleted the fix_previously_silent_error branch April 25, 2025 08:02
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen