Skip to content

Document RSeQC inner_distance limitation for large chromosomes #1624

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Open
wants to merge 1 commit into
base: dev
Choose a base branch
from
Open

Document RSeQC inner_distance limitation for large chromosomes #1624

wants to merge 1 commit into from

Conversation

@pinin4fjords
Copy link
Member

@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 <[email protected]>
@pinin4fjords pinin4fjords force-pushed the docs-rseqc-large-chromosome-limitation branch from e4a3330 to e4ee614 Compare November 14, 2025 17:00
@github-actions
Copy link

github-actions bot commented Nov 14, 2025 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e4ee614

+| ✅ 286 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   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 passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-11-14 17:03:31

@pinin4fjords pinin4fjords added this to the 3.22.0 milestone Nov 14, 2025
@pinin4fjords pinin4fjords mentioned this pull request Nov 14, 2025
Closed
@pinin4fjords
Copy link
Member Author

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

3.22.0

Development

Successfully merging this pull request may close these issues.

2 participants

@pinin4fjords