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Fix --gtf_extra_attributes to support multiple comma-separated values #1635

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pinin4fjords merged 2 commits into from
Nov 25, 2025
Merged

Fix --gtf_extra_attributes to support multiple comma-separated values #1635

pinin4fjords merged 2 commits into from
Nov 25, 2025
+116 −25

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@pinin4fjords pinin4fjords commented Nov 25, 2025

Summary

Fixes #1626

This PR addresses two issues reported:

  1. Primary fix: The --gtf_extra_attributes parameter now correctly supports multiple comma-separated values (e.g., --gtf_extra_attributes gene_name,gene_type). Previously, only single values worked.

  2. Secondary fix: Corrected deprecated parameter name in documentation (--gtf_group_features_type → --featurecounts_group_type).

Changes

Output format change

When using multiple extra attributes, the tx2gene.tsv output now includes a column for each attribute:

Before (single attribute gene_name):

transcript_id	gene_id	gene_name
ENST00001	ENSG00001	TP53

After (multiple attributes gene_name,gene_type):

transcript_id	gene_id	gene_name	gene_type
ENST00001	ENSG00001	TP53	protein_coding

Test plan

  • Module tests pass in nf-core/modules
  • Pipeline CI tests

Thanks to @ahwanpandey for reporting this issue!

🤖 Generated with Claude Code

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github-actions bot commented Nov 25, 2025

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @pinin4fjords,

It looks like this pull-request is has been made against the nf-core/rnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/rnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@pinin4fjords @claude
Fix --gtf_extra_attributes to support multiple comma-separated values
de36ea4 
- Update custom/tx2gene module to parse comma-separated extra attributes
- Fix deprecated parameter name in docs (`--gtf_group_features_type` → `--featurecounts_group_type`)

Fixes #1626

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
@pinin4fjords pinin4fjords force-pushed the fix-gtf-extra-attributes-multiple-values branch from 01f696f to de36ea4 Compare November 25, 2025 21:50
@pinin4fjords pinin4fjords changed the base branch from master to dev November 25, 2025 21:51
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github-actions bot commented Nov 25, 2025 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7c1834e

+| ✅ 284 tests passed       |+
#| ❔   8 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   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 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 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
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/rnaseq/rnaseq/subworkflows/local/prepare_genome/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-11-25 21:55:33

@pinin4fjords pinin4fjords merged commit d3e2124 into dev Nov 25, 2025
34 checks passed
@pinin4fjords pinin4fjords deleted the fix-gtf-extra-attributes-multiple-values branch November 25, 2025 22:13
@pinin4fjords pinin4fjords mentioned this pull request Nov 26, 2025
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@pinin4fjords pinin4fjords mentioned this pull request Dec 8, 2025
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@maxulysse maxulysse maxulysse approved these changes

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Successfully merging this pull request may close these issues.

"--gtf_extra_attributes" only works by giving one attribute and not comma separated multiple values

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