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Merge prepare_genome subworkflows into a single prepare_genome - #162

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feat/prepare-genome-merge
Oct 21, 2026
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Merge prepare_genome subworkflows into a single prepare_genome#162
maxulysse merged 3 commits into
devfrom
feat/prepare-genome-merge

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@maxulysse maxulysse commented Oct 21, 2026

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PR checklist

  • This comment contains a description of changes (for why/what changed, see CONTRIBUTING.md)
  • Container version(s) are updated/rebuilt and pin changed software (if needed)
  • CHANGELOG.md is updated
  • nextflow_schema.json is updated (if needed)
  • docs/usage.md is updated (if needed)
  • docs/output.md is updated (if needed)
  • assets/ is updated (if needed)
  • Remove all TODO comments
  • Test this locally and/or on CI (particularly with GPU/singularity tests)
  • For modules: nf-core/modules PR along with basic tests on Linux, macOS and Windows
  • For pipelines: template update at nf-core/tools along with basic tests (stub run on all profiles)

Description

Merge PREPARE_GENOME_RNASEQ and PREPARE_GENOME_DNASEQ into a single PREPARE_GENOME subworkflow (roadmap PR 7).

  • The two SAMTOOLS_FAIDX invocations collapse into one call with the union of their conditions (('faidx' in tools || 'sizes' in tools) && meta.run_faidx, with generate_sizes driven by sizes). The DNA condition was a strict subset of the RNA one, so behaviour is preserved, and duplicate faidx runs on the same genome no longer happen.
  • workflows/references.nf includes and calls the subworkflow once; all emit names are unchanged, so no downstream wiring or main.nf change was needed.
  • join_by_meta_id moves into the merged subworkflow.
  • Statement order inside the workflow body preserves the original dependencies: HISAT2_BUILD and STAR_GENOMEGENERATE consume the gffread-mixed gtf and the splice-sites mix, so they stay after those mixes.

Scope note: the merged subworkflow is internal. It is not published to the registry and is not part of the consumer contract; consumers keep using the generated params.yml.

Testing

  • nextflow lint clean on the touched files; prek hooks pass.
  • nf-core pipelines lint: 364 passed, 0 failed (21 pre-existing template TODO warnings).
  • nf-test test tests/ --profile=+docker: 19/26 passing. The 7 remaining failures are pre-existing and unrelated: they fail on dev too (dev CI is red), caused by splice_sites URL strings from references-datasheets reaching the output block, on dataflow identical to dev.

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@maxulysse
Merge prepare_genome subworkflows into a single prepare_genome
1f966fb 
Combine PREPARE_GENOME_RNASEQ and PREPARE_GENOME_DNASEQ into one
PREPARE_GENOME subworkflow. The two SAMTOOLS_FAIDX invocations collapse
into one call with the union of their conditions, and
workflows/references.nf calls the subworkflow once.

Generated by OpenCode
@github-actions

github-actions Bot commented Oct 21, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b0ff179

+| ✅ 216 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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 output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • 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 base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-10-21 11:42:29

@nf-core nf-core deleted a comment from github-actions Bot Oct 21, 2026
@maxulysse
Resolve datasheet splice_sites paths to files
b0ff179 
Nextflow 26.10 publish no longer coerces strings, so the raw URL string
in the splice_sites channel crashed the output block with
'No such variable: fileName'. Resolve it like every other datasheet field.

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@nf-core nf-core deleted a comment from github-actions Bot Oct 21, 2026
@maxulysse
maxulysse merged commit a2385b4 into dev Oct 21, 2026
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@maxulysse
maxulysse deleted the feat/prepare-genome-merge branch October 21, 2026 12:53
@maxulysse maxulysse mentioned this pull request Oct 21, 2026
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