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Prerelease 3.14.0 fixes #1154

Merged
merged 7 commits into from
Jan 5, 2024
Merged

Prerelease 3.14.0 fixes #1154

merged 7 commits into from
Jan 5, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Jan 4, 2024 •
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In this PR:

  • Disable an additional versions section that had crept it with recent MultiQC
  • Reorder preprocessing to delay strand inference until after filtering
  • Fix conditional publishing to avoid empty directories
  • Bump versions

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/rnaseq 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).

@pinin4fjords pinin4fjords marked this pull request as draft January 4, 2024 16:42
@pinin4fjords pinin4fjords changed the title Prerelease 3.14.0 fixes [WIP] Prerelease 3.14.0 fixes Jan 4, 2024
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github-actions bot commented Jan 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f06f298

+| ✅ 145 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: 3.14.0
  • 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 WorkflowRnaseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-05 09:51:14

@pinin4fjords pinin4fjords mentioned this pull request Jan 4, 2024
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@pinin4fjords pinin4fjords changed the title [WIP] Prerelease 3.14.0 fixes Prerelease 3.14.0 fixes Jan 4, 2024
@pinin4fjords pinin4fjords marked this pull request as ready for review January 4, 2024 18:38
drpatelh
drpatelh reviewed Jan 5, 2024
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@drpatelh drpatelh mentioned this pull request Jan 5, 2024
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drpatelh
drpatelh approved these changes Jan 5, 2024
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👌🏽

@drpatelh drpatelh merged commit 7ab1724 into dev Jan 5, 2024
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@drpatelh drpatelh deleted the prerelease_3.14.0_fixes branch January 21, 2024 09:38
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