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Merged
pinin4fjords merged 19 commits into from
Jun 9, 2025
Merged

Improve reproducibility with Conda #1565

pinin4fjords merged 19 commits into from
Jun 9, 2025

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@pinin4fjords pinin4fjords commented Jun 6, 2025

#1564 is mis-reporting the version for perl in this module. Let's see if a stricter pin solves it.

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 pipelines 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 Jun 6, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ed0602f

+| ✅ 277 tests passed       |+
#| ❔   7 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: 3.19.0
  • 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 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 nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-06-09 15:11:44

@pinin4fjords pinin4fjords changed the title try to fix perl version mis-reporting Improve reproducibility with Conda Jun 6, 2025
@pinin4fjords pinin4fjords enabled auto-merge June 9, 2025 15:09
@pinin4fjords pinin4fjords merged commit 7dd5ea8 into dev Jun 9, 2025
7 of 35 checks passed
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pinin4fjords commented Jun 9, 2025

NB: for some reason auto-merge merged this before final tests completed (I killed them after), but I'm sure it was all good.

@pinin4fjords pinin4fjords mentioned this pull request Jun 9, 2025
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@maxulysse maxulysse maxulysse approved these changes

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