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Add ribocode to workflow mimicking ribotricer implementation #136

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Merged
JackCurragh merged 13 commits into from
Jan 14, 2026
Merged

Add ribocode to workflow mimicking ribotricer implementation #136

JackCurragh merged 13 commits into from
Jan 14, 2026

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@JackCurragh JackCurragh commented Dec 16, 2025

add RiboCode for calling translated regions. - #132

  • Add RiboCode modules (gtfupdate, prepare, metaplots, ribocode)
  • Integrate 4-step RiboCode workflow in workflows/riboseq/main.nf
  • Update documentation and schema
  • Skip RiboCode in basic tests (like Ribotricer)

Running test_full currently

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 contribution docs
  • If necessary, also make a PR on the nf-core/riboseq branch on the 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 <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <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).

pinin4fjords
pinin4fjords reviewed Dec 16, 2025
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pinin4fjords
pinin4fjords reviewed Dec 16, 2025
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github-actions bot commented Jan 13, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 53cd1b5

+| ✅ 269 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!
Details

❗ Test warnings:

  • 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_if_empty_null - ifEmpty(null) found in /home/runner/work/riboseq/riboseq/subworkflows/local/prepare_genome/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • nf_test_content - nf_test_content
  • files_unchanged - File ignored due to lint config: assets/nf-core-riboseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-riboseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-riboseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-01-14 10:35:46

pinin4fjords and others added 3 commits January 13, 2026 14:24
@pinin4fjords @claude
Fix trailing whitespace in CITATIONS.md for prettier
2fd7ec8 
Co-Authored-By: Claude Opus 4.5 <[email protected]>
@pinin4fjords @claude
Merge branch 'dev' into feat/add-ribocode
6fab42d 
Resolve conflicts to integrate plastid P-site identification alongside
RiboCode ORF detection. Both features are now available in the pipeline.

Co-Authored-By: Claude Opus 4.5 <[email protected]>
@pinin4fjords @claude
Fix schema path and simplify RiboCode channel logic
53cd1b5 
- Revert hardcoded local path in nextflow_schema.json back to
  ${projectDir}/assets/rrna-db-defaults.txt
- Simplify RiboCode workflow channel handling by removing unnecessary
  intermediate tuple construction

Co-Authored-By: Claude Opus 4.5 <[email protected]>
@JackCurragh JackCurragh merged commit 9e21ee6 into dev Jan 14, 2026
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@JackCurragh @pinin4fjords