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chore: clean up inapplicable lint warnings - #381

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nictru merged 1 commit into
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chore/clean-lint-warnings
Oct 28, 2026
Merged

chore: clean up inapplicable lint warnings#381
nictru merged 1 commit into
devfrom
chore/clean-lint-warnings

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@nictru

@nictru nictru commented Oct 28, 2026

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Summary

Exclude unused reference-genome configuration files from lint checks. This pipeline does not require a reference genome. Remove the two template TODO comments in the resource configuration without changing resource settings.

 .nf-core.yml: lint.files_exist
+  conf/igenomes.config
+  conf/igenomes_ignored.config
 conf/base.config
-  TODO: Check the defaults for all processes
-  TODO: Customise requirements for specific processes

Leave Zenodo and release placeholders, and the AWS full-test TODO, unchanged.

Evidence

  • Before: two missing iGenomes file warnings and two resource-configuration TODO warnings.
  • After: both paths are excluded using the documented nf-core/tools 4.2.1 configuration; both TODO comments are removed.
  • prek and git diff --cached --check passed.
  • nf-core pipelines lint and pipeline tests were skipped with user approval because nf-core and nf-test are unavailable in the shell. The warning reduction awaits CI verification.

Merge Danger

Door: two-way

Blast Radius: lint

No pipeline runtime settings change.

Generated by GPT-6.1 Sol

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core pipelines lint). Local check skipped with user approval; awaiting CI.
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>). Local check skipped with user approval.

@nictru
chore: clean up inapplicable lint warnings
431fdfd 
Exclude unused iGenomes configuration files from existence checks and remove resource configuration TODO comments. Leave runtime settings and release placeholders unchanged.

Generated by GPT-6.1 Sol
@github-actions

github-actions Bot commented Oct 28, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 431fdfd

+| ✅ 331 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in CHANGELOG.md: ## v0.0.1dev - [unreleased replace with date on release ]
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 4.2.1
  • Run at 2026-10-28 17:24:07

@nictru
nictru merged commit 0048567 into dev Oct 28, 2026
6 checks passed
@nictru
nictru deleted the chore/clean-lint-warnings branch October 28, 2026 17:43
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