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Fix default for umi_discard_read to prevent validation errors in Platform #1605

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Merged
Parent: Dev -> Master for 3.21.0
merged 2 commits into from
Sep 17, 2025
Merged

Fix default for umi_discard_read to prevent validation errors in Platform #1605

merged 2 commits into from
Sep 17, 2025

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@pinin4fjords pinin4fjords commented Sep 17, 2025 •
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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).

@pinin4fjords pinin4fjords linked an issue Sep 17, 2025 that may be closed by this pull request
umi_discard_read validation fails in Seqera Platform #1600
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@pinin4fjords pinin4fjords changed the title Fix default for umi_discard_read to prevent validation errors in Plat… Fix default for umi_discard_read to prevent validation errors in Platform Sep 17, 2025
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github-actions bot commented Sep 17, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ef4c511

+| ✅ 290 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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 nextflow.config: Specify any additional parameters here
  • 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_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 3.3.2
  • Run at 2025-09-17 10:26:54

@pinin4fjords pinin4fjords merged commit c003e2d into dev Sep 17, 2025
34 checks passed
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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umi_discard_read validation fails in Seqera Platform

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@pinin4fjords @FriederikeHanssen