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Fix MultiQC report generation #145

Merged
merged 2 commits into from
Oct 17, 2023
Merged

Fix MultiQC report generation #145

merged 2 commits into from
Oct 17, 2023

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Aratz
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@Aratz Aratz commented Oct 17, 2023 •
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A bug was introduced in #132: the MultiQC file channel was flushed empty before the report was constructed. This led to empty reports. This PR fixes this issue.

Fixes #64, fixes #144

NB: linting tests fail but I suspect it's because of the v2.10 template update, should be fixed once #141 is reviewed and merged.

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!
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

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github-actions bot commented Oct 17, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9236c6f

+| ✅ 156 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowDemultiplex.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-17 11:21:21

@Aratz Aratz marked this pull request as ready for review October 17, 2023 06:44
@Aratz Aratz merged commit 3df96fc into nf-core:dev Oct 17, 2023
6 checks passed
@Aratz Aratz self-assigned this Oct 18, 2023
@edmundmiller edmundmiller added this to the 1.4.0 milestone Oct 18, 2023
@Aratz Aratz mentioned this pull request Dec 14, 2023
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

@matthdsm matthdsm matthdsm approved these changes

@edmundmiller edmundmiller Awaiting requested review from edmundmiller

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@Aratz Aratz

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Hackathon: November 2023
Status: Done
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1.4.0
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@Aratz @matthdsm @adamrtalbot @edmundmiller