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Merged
pinin4fjords merged 3 commits into from
Dec 5, 2025
Merged

Add dupMatrix files to nftignore for reproducibility #1651

pinin4fjords merged 3 commits into from
Dec 5, 2025
+2 −58

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@pinin4fjords pinin4fjords commented Dec 5, 2025

Summary

  • Add {hisat2,star_rsem,star_salmon}/dupradar/gene_data/*_dupMatrix.txt pattern to .nftignore
  • Remove md5 checksums for *_dupMatrix.txt files from all snapshot files

Context

DupRadar's dupMatrix.txt output files exhibit non-reproducible content due to conda dependency drift, causing intermittent CI test failures on ARM (see failed run).

The file content varies between environments while still being functionally correct, so we exclude these files from md5 verification while keeping them in the file existence checks.

Test plan

  • ARM CI tests pass without dupMatrix md5 mismatches

🤖 Generated with Claude Code

@pinin4fjords @claude
Add dupMatrix files to nftignore for reproducibility
e7a8e17 
DupRadar's dupMatrix output files have non-reproducible content due to
conda dependency drift, causing ARM CI test failures. Adding these files
to .nftignore and removing their md5 checksums from snapshot files.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
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github-actions bot commented Dec 5, 2025

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @pinin4fjords,

It looks like this pull-request is has been made against the nf-core/rnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/rnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@pinin4fjords @claude
Update changelog for PR #1651
e72e572 
🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
@pinin4fjords pinin4fjords changed the base branch from master to dev December 5, 2025 16:51
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github-actions bot commented Dec 5, 2025 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3ffe0ee

+| ✅ 284 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 3.22.1
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 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 nextflow.config: Specify any additional parameters here
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/rnaseq/rnaseq/subworkflows/local/prepare_genome/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-12-05 16:54:56

@pinin4fjords pinin4fjords merged commit 19482e0 into dev Dec 5, 2025
85 of 94 checks passed
@pinin4fjords pinin4fjords deleted the fix/dupmatrix-nftignore branch December 5, 2025 17:46
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