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refactor: compose test_prokaryotic profile on prokaryotic #1734

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Merged
pinin4fjords merged 4 commits into from
Feb 27, 2026
Merged

refactor: compose test_prokaryotic profile on prokaryotic #1734

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2babe57
refactor: compose test_prokaryotic profile on prokaryotic
pinin4fjords Feb 27, 2026
bd06b4a
Merge branch 'dev' into fix/prokaryotic-profile-composability
pinin4fjords Feb 27, 2026
c7ca5e5
docs: add PR #1734 to changelog
pinin4fjords Feb 27, 2026
b91f906
Merge branch 'dev' into fix/prokaryotic-profile-composability
pinin4fjords Feb 27, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -55,6 +55,7 @@ Special thanks to the following for their contributions to the release:
- [PR #1725](https://github.com/nf-core/rnaseq/pull/1725) - Refine .nftignore patterns to reinstate tx2gene MD5 checking, remove redundant UNTAR version collection
- [PR #1728](https://github.com/nf-core/rnaseq/pull/1728) - Re-render metro map with nf-metro v0.5.4: bolder section labels and number badges for improved visual hierarchy, increased vertical spacing between stacked sections, synchronized animation timing
- [PR #1730](https://github.com/nf-core/rnaseq/pull/1730) - Bump Nextflow from 25.04.0 to 25.04.3 in CI to fix `conda create --mkdir` failure ([nextflow-io/nextflow#5947](https://github.com/nextflow-io/nextflow/issues/5947))
- [PR #1734](https://github.com/nf-core/rnaseq/pull/1734) - Compose `test_prokaryotic` profile on `prokaryotic` to remove duplicated settings
- [PR #1735](https://github.com/nf-core/rnaseq/pull/1735) - Code quality improvements: replace opaque tuple indexing with named destructuring, rename `ch_dummy_file`, move metro map docs, align GPU CI workflow with other workflows

### Parameters
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19 changes: 3 additions & 16 deletions conf/test_prokaryotic.config
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Expand Up @@ -8,6 +8,9 @@
Use as follows:
nextflow run nf-core/rnaseq -profile test_prokaryotic,<docker/singularity> --outdir <OUTDIR>

Note: test_prokaryotic composes on the prokaryotic profile (via nextflow.config),
so core prokaryotic settings are inherited automatically.

----------------------------------------------------------------------------------------
*/

Expand All @@ -33,22 +36,6 @@ params {
transcript_fasta = null
additional_fasta = null

// Prokaryotic-specific settings
prokaryotic = true
gffread_transcript_fasta = true
featurecounts_feature_type = 'CDS'

// Default aligner for prokaryotes (can be overridden with --aligner star_salmon)
aligner = 'bowtie2_salmon'

// Skip bigwig for bowtie2_salmon (aligns to transcriptome, not genome)
skip_bigwig = true

// Skip QC tools that assume eukaryotic features
skip_rseqc = true
skip_dupradar = true
skip_qualimap = true

// Skip steps not needed for minimal testing
skip_bbsplit = true
skip_preseq = true
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5 changes: 4 additions & 1 deletion nextflow.config
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Expand Up @@ -288,7 +288,10 @@ profiles {
}
}
test_full { includeConfig 'conf/test_full.config' }
test_prokaryotic { includeConfig 'conf/test_prokaryotic.config' }
test_prokaryotic {
includeConfig 'conf/prokaryotic.config'
includeConfig 'conf/test_prokaryotic.config'
}
prokaryotic { includeConfig 'conf/prokaryotic.config' }
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@adamrtalbot adamrtalbot Feb 27, 2026

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Poor prokaryotic profile feels out of place down here with all the test profiles 😆

test_full_aws {
includeConfig 'conf/test_full.config'
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