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docs: clarify GFF files must use --gff parameter#1751

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pinin4fjords merged 2 commits intodevfrom
fix/gtf-gff-schema-guidance
Mar 24, 2026
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docs: clarify GFF files must use --gff parameter#1751
pinin4fjords merged 2 commits intodevfrom
fix/gtf-gff-schema-guidance

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@pinin4fjords pinin4fjords commented Mar 24, 2026

Summary

  • Clarifies in the "GTF vs GFF" docs section that GFF3 files must be provided via --gff and GTF files via --gtf, since schema validation enforces file extensions per parameter
  • Fixes the prokaryotic docs section that incorrectly implied --gtf also accepts GFF files

Closes #1584

Test plan

  • Verify docs render correctly on the nf-core website

🤖 Generated with Claude Code

pinin4fjords and others added 2 commits March 24, 2026 10:31
@pinin4fjords @claude
docs: clarify that GFF files must use --gff parameter, not --gtf
27ec40d 
Users were passing GFF/GFF3 files to --gtf and getting validation
errors. Updated docs to make it clear that --gtf only accepts GTF
files and --gff should be used for GFF3 files.

Closes #1584

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@pinin4fjords @claude
chore: update changelog PR number to #1751
00bfba1 
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@pinin4fjords pinin4fjords mentioned this pull request Mar 24, 2026
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nf-core-bot commented Mar 24, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Mar 24, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 00bfba1

+| ✅ 203 tests passed       |+
#| ❔   9 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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 base.config: Check the defaults for all processes
  • 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!

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-03-24 10:34:59

@pinin4fjords pinin4fjords merged commit 2bb2f65 into dev Mar 24, 2026
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pinin4fjords commented Mar 24, 2026

Thanks again @maxulysse !

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@maxulysse maxulysse maxulysse approved these changes

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