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Merged
merged 3 commits into from
Nov 25, 2025
Merged

Document RSeQC inner_distance limitation for large chromosomes #1624

merged 3 commits into from
Nov 25, 2025
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@pinin4fjords pinin4fjords commented Nov 14, 2025

Summary

This PR documents a known limitation in the RSeQC inner_distance module that affects genomes with chromosomes exceeding ~537 million bases, such as plant genomes (wheat, barley, etc.).

Changes

  • Added new section "Large chromosomes (plant genomes)" to docs/usage.md
  • Explains the bx-python BitSet limitation
  • Provides clear workaround using --rseqc_modules parameter
  • References upstream issues for additional context

Context

This addresses issue #608, which has been open since 2021. The underlying issue is in the bx-python library and remains unresolved upstream (see bxlab/bx-python#67). This documentation change helps users understand and work around the limitation.

Test plan

  • Documentation builds correctly
  • Workaround command syntax is accurate
  • Links to upstream issues are valid

Closes #608

🤖 Generated with Claude Code

@pinin4fjords @claude
Document RSeQC inner_distance limitation for large chromosomes
e4ee614 
Add documentation explaining the bx-python BitSet limitation that affects
genomes with chromosomes >500 Mb (commonly plant genomes). Provide clear
workaround by excluding inner_distance from rseqc_modules parameter.

Closes #608

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

Co-Authored-By: Claude <noreply@anthropic.com>
@pinin4fjords pinin4fjords force-pushed the docs-rseqc-large-chromosome-limitation branch from e4a3330 to e4ee614 Compare November 14, 2025 17:00
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github-actions bot commented Nov 14, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c43fdba

+| ✅ 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 17:30:35

@pinin4fjords pinin4fjords added this to the 3.22.0 milestone Nov 14, 2025
@pinin4fjords pinin4fjords mentioned this pull request Nov 14, 2025
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pinin4fjords commented Nov 14, 2025

Note: CI is currently failing due to an issue with the nf-core lint check that has been fixed in PR #1618, which is awaiting approval. This PR's changes are ready for review once that merge is complete.

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nf-core-bot commented Nov 25, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.4.1.
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.

@pinin4fjords pinin4fjords merged commit a9f031d into dev Nov 25, 2025
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@pinin4fjords pinin4fjords deleted the docs-rseqc-large-chromosome-limitation branch November 25, 2025 17:33
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