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Merged
pinin4fjords merged 10 commits into from
Dec 11, 2025
Merged

Reduce duplicate coverage in pipeline tests #1648

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1e1c471
test: reduce duplicate coverage in pipeline tests
pinin4fjords Dec 4, 2025
5f60ca9
update snaps
pinin4fjords Dec 4, 2025
85e4f77
Try to spoof sentieon snap
pinin4fjords Dec 4, 2025
ee6f3fa
Try again to spoof sentieon snap
pinin4fjords Dec 4, 2025
7a189b2
Merge branch 'dev' into test/reduce-duplicate-coverage
pinin4fjords Dec 11, 2025
9e71a50
Bump snaps
pinin4fjords Dec 11, 2025
d38359f
Merge branch 'dev' into test/reduce-duplicate-coverage
pinin4fjords Dec 11, 2025
c43266c
snap fixes
pinin4fjords Dec 11, 2025
3f91fda
Another snap fix
pinin4fjords Dec 11, 2025
2f2db63
docs: add changelog entry for PR #1648
pinin4fjords Dec 11, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [PR #1656](https://github.com/nf-core/rnaseq/pull/1656) - Bump version after release 3.22.1
- [PR #1658](https://github.com/nf-core/rnaseq/pull/1658) - Bump nf-core/multiqc module to 1.33
- [PR #1660](https://github.com/nf-core/rnaseq/pull/1660) - Update MultiQC ARM container to 1.33
- [PR #1648](https://github.com/nf-core/rnaseq/pull/1648) - Reduce duplicate coverage in pipeline tests by adding skip options

## [[3.22.1](https://github.com/nf-core/rnaseq/releases/tag/3.22.1)] - 2025-12-04

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2 changes: 1 addition & 1 deletion tests/default.nf.test.snap
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Expand Up @@ -1489,4 +1489,4 @@
},
"timestamp": "2025-08-12T11:31:43.21579283"
}
}
}
8 changes: 8 additions & 0 deletions tests/featurecounts_group_type.nf.test
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Expand Up @@ -10,6 +10,10 @@ nextflow_pipeline {
params {
outdir = "$outputDir"
featurecounts_group_type = false
// Skip processes already covered by default.nf.test (featureCounts grouping doesn't affect BAMs)
skip_qc = true
skip_stringtie = true
skip_bigwig = true
}
}

Expand Down Expand Up @@ -42,6 +46,10 @@ nextflow_pipeline {
params {
outdir = "$outputDir"
featurecounts_group_type = false
// Skip processes already covered by default.nf.test (featureCounts grouping doesn't affect BAMs)
skip_qc = true
skip_stringtie = true
skip_bigwig = true
}
}

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731 changes: 10 additions & 721 deletions tests/featurecounts_group_type.nf.test.snap
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@LouisLeNezet LouisLeNezet Dec 11, 2025

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This is indeed quite a lot of changes !

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@pinin4fjords pinin4fjords Dec 11, 2025

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Yes! The principle here is that --featurecounts_group_type only affects how featureCounts groups counts (gene vs transcript level) - it doesn't change the BAM files at all. So running QC, StringTie, and BigWig generation on identical BAMs is redundant with default.nf.test.

The test still covers:

  • The full alignment pathway (STAR → BAM → Salmon)
  • featureCounts with the modified grouping parameter
  • All the quantification outputs

We're just skipping the BAM-consuming processes that would produce identical results to the default test. The snapshot reduction is dramatic because those QC/StringTie/BigWig outputs were a large portion of what was being captured.

Large diffs are not rendered by default.

6 changes: 6 additions & 0 deletions tests/hisat2.nf.test
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Expand Up @@ -10,6 +10,9 @@ nextflow_pipeline {
params {
outdir = "$outputDir"
aligner = 'hisat2'
// Skip bigwig (coverage tracks don't vary meaningfully by aligner)
// Keep QC and StringTie as HISAT2 BAMs have different characteristics worth integration testing
skip_bigwig = true
}
}

Expand Down Expand Up @@ -42,6 +45,9 @@ nextflow_pipeline {
params {
outdir = "$outputDir"
aligner = 'hisat2'
// Skip bigwig (coverage tracks don't vary meaningfully by aligner)
// Keep QC and StringTie as HISAT2 BAMs have different characteristics worth integration testing
skip_bigwig = true
}
}

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30 changes: 5 additions & 25 deletions tests/hisat2.nf.test.snap
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Expand Up @@ -104,14 +104,11 @@
},
"Params: --aligner hisat2": {
"content": [
205,
175,
{
"BBMAP_BBSPLIT": {
"bbmap": 39.18
},
"BEDTOOLS_GENOMECOV_FW": {
"bedtools": "2.31.1"
},
"CAT_FASTQ": {
"cat": 9.5
},
Expand Down Expand Up @@ -230,12 +227,6 @@
"TXIMETA_TXIMPORT": {
"bioconductor-tximeta": "1.20.1"
},
"UCSC_BEDCLIP": {
"ucsc": 377
},
"UCSC_BEDGRAPHTOBIGWIG": {
"ucsc": 469
},
"UNTAR_HISAT2_INDEX": {
"untar": 1.34
},
Expand Down Expand Up @@ -319,17 +310,6 @@
"hisat2/WT_REP1.markdup.sorted.bam.bai",
"hisat2/WT_REP2.markdup.sorted.bam",
"hisat2/WT_REP2.markdup.sorted.bam.bai",
"hisat2/bigwig",
"hisat2/bigwig/RAP1_IAA_30M_REP1.forward.bigWig",
"hisat2/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig",
"hisat2/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig",
"hisat2/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig",
"hisat2/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig",
"hisat2/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig",
"hisat2/bigwig/WT_REP1.forward.bigWig",
"hisat2/bigwig/WT_REP1.reverse.bigWig",
"hisat2/bigwig/WT_REP2.forward.bigWig",
"hisat2/bigwig/WT_REP2.reverse.bigWig",
"hisat2/dupradar",
"hisat2/dupradar/box_plot",
"hisat2/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf",
Expand Down Expand Up @@ -1331,9 +1311,9 @@
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-08-12T11:48:58.018707447"
"timestamp": "2025-12-04T15:43:24.360940596"
}
}
}
3 changes: 2 additions & 1 deletion tests/kallisto.nf.test.snap
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Expand Up @@ -336,6 +336,7 @@
"trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt"
],
[

]
],
"meta": {
Expand All @@ -344,4 +345,4 @@
},
"timestamp": "2025-01-28T13:50:34.753130451"
}
}
}
8 changes: 8 additions & 0 deletions tests/min_mapped_reads.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,10 @@ nextflow_pipeline {
params {
outdir = "$outputDir"
min_mapped_reads = 90
// Skip processes already covered by default.nf.test (sample filtering doesn't change BAM structure)
skip_qc = true
skip_stringtie = true
skip_bigwig = true
}
}

Expand Down Expand Up @@ -42,6 +46,10 @@ nextflow_pipeline {
params {
outdir = "$outputDir"
min_mapped_reads = 90
// Skip processes already covered by default.nf.test (sample filtering doesn't change BAM structure)
skip_qc = true
skip_stringtie = true
skip_bigwig = true
}
}

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