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

test: load prokaryotic config in nf-test instead of duplicating params #1736

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6b76036
test: load prokaryotic config in nf-test instead of duplicating params
pinin4fjords Feb 27, 2026
e3d5469
docs: add PR #1736 to changelog
pinin4fjords Feb 27, 2026
4e5e748
test: remove prokaryotic snapshots for regeneration
pinin4fjords Feb 27, 2026
f8927b3
test: update prokaryotic star_salmon snapshot for skip_bigwig
pinin4fjords Feb 27, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@ Special thanks to the following for their contributions to the release:
- [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
- [PR #1736](https://github.com/nf-core/rnaseq/pull/1736) - Load prokaryotic config in nf-test instead of duplicating params in each test

### Parameters

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83 changes: 23 additions & 60 deletions tests/prokaryotic.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ nextflow_pipeline {

name "Test pipeline with prokaryotic settings"
script "../main.nf"
config "../conf/prokaryotic.config"
tag "pipeline"
tag "prokaryotic"

Expand All @@ -21,23 +22,15 @@ nextflow_pipeline {
transcript_fasta = null
additional_fasta = null

// Prokaryotic-specific settings
prokaryotic = true
gffread_transcript_fasta = true
// Override aligner (prokaryotic profile defaults to bowtie2_salmon)
aligner = 'star_salmon'
featurecounts_feature_type = 'CDS'

// Skip eukaryote-specific QC tools
skip_rseqc = true
skip_dupradar = true
skip_qualimap = true
// Skip steps not needed for minimal testing
skip_bbsplit = true
skip_preseq = true
skip_biotype_qc = true
skip_deseq2_qc = true

// Skip unnecessary steps for faster testing
skip_bbsplit = true
skip_preseq = true
pseudo_aligner = null
skip_deseq2_qc = true
pseudo_aligner = null
min_trimmed_reads = 0
}
}
Expand Down Expand Up @@ -77,23 +70,15 @@ nextflow_pipeline {
transcript_fasta = null
additional_fasta = null

// Prokaryotic-specific settings
prokaryotic = true
gffread_transcript_fasta = true
// Override aligner (prokaryotic profile defaults to bowtie2_salmon)
aligner = 'star_salmon'
featurecounts_feature_type = 'CDS'

// Skip eukaryote-specific QC tools
skip_rseqc = true
skip_dupradar = true
skip_qualimap = true
// Skip steps not needed for minimal testing
skip_bbsplit = true
skip_preseq = true
skip_biotype_qc = true
skip_deseq2_qc = true

// Skip unnecessary steps for faster testing
skip_bbsplit = true
skip_preseq = true
pseudo_aligner = null
skip_deseq2_qc = true
pseudo_aligner = null
min_trimmed_reads = 0
}
}
Expand Down Expand Up @@ -135,23 +120,12 @@ nextflow_pipeline {
transcript_fasta = null
additional_fasta = null

// Prokaryotic-specific settings
gffread_transcript_fasta = true
aligner = 'bowtie2_salmon'
skip_bigwig = true
featurecounts_feature_type = 'CDS'

// Skip eukaryote-specific QC tools
skip_rseqc = true
skip_dupradar = true
skip_qualimap = true
// Skip steps not needed for minimal testing
skip_bbsplit = true
skip_preseq = true
skip_biotype_qc = true
skip_deseq2_qc = true

// Skip unnecessary steps for faster testing
skip_bbsplit = true
skip_preseq = true
pseudo_aligner = null
skip_deseq2_qc = true
pseudo_aligner = null
min_trimmed_reads = 0
}
}
Expand Down Expand Up @@ -191,23 +165,12 @@ nextflow_pipeline {
transcript_fasta = null
additional_fasta = null

// Prokaryotic-specific settings
gffread_transcript_fasta = true
aligner = 'bowtie2_salmon'
skip_bigwig = true
featurecounts_feature_type = 'CDS'

// Skip eukaryote-specific QC tools
skip_rseqc = true
skip_dupradar = true
skip_qualimap = true
// Skip steps not needed for minimal testing
skip_bbsplit = true
skip_preseq = true
skip_biotype_qc = true
skip_deseq2_qc = true

// Skip unnecessary steps for faster testing
skip_bbsplit = true
skip_preseq = true
pseudo_aligner = null
skip_deseq2_qc = true
pseudo_aligner = null
min_trimmed_reads = 0
}
}
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19 changes: 1 addition & 18 deletions tests/prokaryotic.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,14 +1,8 @@
{
"Params: --aligner star_salmon --prokaryotic": {
"content": [
58,
46,
{
"BEDTOOLS_GENOMECOV_FW": {
"bedtools": "2.31.1"
},
"BEDTOOLS_GENOMECOV_REV": {
"bedtools": "2.31.1"
},
"CUSTOM_TX2GENE": {
"python": "3.10.4"
},
Expand Down Expand Up @@ -82,12 +76,6 @@
"TXIMETA_TXIMPORT": {
"bioconductor-tximeta": "1.20.1"
},
"UCSC_BEDCLIP": {
"ucsc": 377
},
"UCSC_BEDGRAPHTOBIGWIG": {
"ucsc": 469
},
"UNTAR_SALMON_INDEX": {
"untar": 1.34
}
Expand Down Expand Up @@ -347,11 +335,6 @@
"star_salmon/SALM_REP2/logs/salmon_quant.log",
"star_salmon/SALM_REP2/quant.genes.sf",
"star_salmon/SALM_REP2/quant.sf",
"star_salmon/bigwig",
"star_salmon/bigwig/SALM_REP1.forward.bigWig",
"star_salmon/bigwig/SALM_REP1.reverse.bigWig",
"star_salmon/bigwig/SALM_REP2.forward.bigWig",
"star_salmon/bigwig/SALM_REP2.reverse.bigWig",
"star_salmon/log",
"star_salmon/log/SALM_REP1.Log.final.out",
"star_salmon/log/SALM_REP1.Log.out",
Expand Down