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Fix: test config profile fails to populate example samplesheet as input#373

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atrigila merged 1 commit intodevfrom
345-test-config-profile-fails-to-populate-example-samplesheet-as-input
Feb 12, 2026
Merged

Fix: test config profile fails to populate example samplesheet as input#373
atrigila merged 1 commit intodevfrom
345-test-config-profile-fails-to-populate-example-samplesheet-as-input

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@atrigila atrigila commented Feb 9, 2026

Closes #345

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/demultiplex 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 Feb 9, 2026

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4dad614

+| ✅ 208 tests passed       |+
#| ❔   1 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in base.config: Customise requirements for specific 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 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

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-02-09 17:29:00

@atrigila atrigila marked this pull request as ready for review February 9, 2026 17:51
@atrigila atrigila requested a review from a team as a code owner February 9, 2026 17:51
@atrigila atrigila requested review from glichtenstein and grst and removed request for a team February 9, 2026 17:51
@atrigila atrigila merged commit 1775474 into dev Feb 12, 2026
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@atrigila atrigila mentioned this pull request Feb 12, 2026
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@grst grst grst approved these changes

@glichtenstein glichtenstein Awaiting requested review from glichtenstein glichtenstein is a code owner automatically assigned from nf-core/demultiplex

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