Update rseqc module and bam_rseqc subworkflow

[adamhowardprice]

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PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md
• If necessary, also make a PR on the nf-core/rnaseq branch on the https://github.com/nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir ).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir ).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

Description

Bug Fix

Updates all RSeQC modules and the bam_rseqc subworkflow from nf-core/modules to fix a bug where RSeQC processes fail with:

[E::idx_find_and_load] Could not retrieve index file for '.markdup.sorted.bam'

The RSeQC tools require BAM index files (.bai) but the previous module versions did not declare them as inputs, causing Nextflow to not stage the index files.

Changes

Pulls updates from nf-core/modules#9546:

• Added BAI input to all RSeQC modules:
  • rseqc/bamstat
  • rseqc/inferexperiment
  • rseqc/innerdistance
  • rseqc/junctionannotation
  • rseqc/junctionsaturation
  • rseqc/readdistribution
  • rseqc/readduplication
  • rseqc/tin
• Updated bam_rseqc subworkflow to pass bam_bai channel to all modules
• Bumped RSeQC from 5.0.3 → 5.0.4
• Bumped r-base from >=3.5 → 4.3
• Migrated to topic-based versions (replaces versions.yml output)
• Updated tests with BAI inputs and proper module tags

No documentation changes required

This is a bug fix with no user-facing parameter or output changes.

[github-actions]

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

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Hi @adamhowardprice,

It looks like this pull-request is has been made against the immunera/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 immunera/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!

[adamhowardprice]

These changes are already reflected on the dev branch. Closed.