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Improved pipeline summary report & error message #680

Merged
merged 5 commits into from
Dec 19, 2023
Merged

Improved pipeline summary report & error message #680

merged 5 commits into from
Dec 19, 2023

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d4straub
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@d4straub d4straub commented Dec 19, 2023 •
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Minor improvements to error messages and pipeline report:

  • one error message referred to --input when it should be --input_folder
  • report folder <outdir>/input only when its actually created (when there is a metadata sheet and/or sample sheet)
  • reporting % discarded reads by cutadapt trimming were not reported (NA) when the percentages were less than 10.0%.

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/ampliseq 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).

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github-actions bot commented Dec 19, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f1ae7cb

+| ✅ 154 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-19 13:01:25

@d4straub
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Thanks! :)

@d4straub d4straub merged commit 709dea9 into nf-core:dev Dec 19, 2023
18 checks passed
@d4straub d4straub deleted the fix-report branch December 19, 2023 13:39
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@d4straub @FriederikeHanssen