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Fix missing version from subworkflow snapshot #9548

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Merged
Aratz merged 1 commit into from
Dec 10, 2025
Merged

Fix missing version from subworkflow snapshot #9548

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1 change: 1 addition & 0 deletions subworkflows/nf-core/bam_create_som_pon_gatk/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@ nextflow_workflow {
then {
assertAll(
{ assert workflow.success },
{ assert snapshot(workflow.out.versions).match("versions") },
{ assert snapshot(file(workflow.out.mutect2_vcf.get(0).get(1)).name).match("test1.vcf.gz") },
{ assert snapshot(file(workflow.out.mutect2_index.get(0).get(1)).name).match("test1.vcf.gz.tbi") },
{ assert snapshot(file(workflow.out.mutect2_stats.get(0).get(1)).name).match("test1.vcf.gz.stats") },
Expand Down
15 changes: 15 additions & 0 deletions subworkflows/nf-core/bam_create_som_pon_gatk/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,21 @@
},
"timestamp": "2024-02-14T06:59:54.102164313"
},
"versions": {
"content": [
[
"versions.yml:md5,372aff89fa24a61afed05026b9300345",
"versions.yml:md5,4e7c726474b7a321e56c5260ad8ab209",
"versions.yml:md5,4e7c726474b7a321e56c5260ad8ab209",
"versions.yml:md5,b21263bb2f8ab5733906245941e30e77"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-12-10T15:46:00.217316738"
},
"test_panel.vcf.gz.tbi": {
"content": [
"test_panel.vcf.gz.tbi"
Expand Down
3 changes: 2 additions & 1 deletion subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -486,7 +486,8 @@ nextflow_workflow {
{ assert bowtie2RrnaCount == 10 }, // 10 reads aligned to rRNA reference
{ assert snapshot(
selines.join('\n').md5(),
processed_ribo_removal_lint_report.md5()
processed_ribo_removal_lint_report.md5(),
workflow.out.versions
).match() }
)
}
Expand Down
19 changes: 15 additions & 4 deletions subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -50,12 +50,23 @@
"homo_sapiens single-end [fastq] fastp bowtie2": {
"content": [
"b423f619ae31c22b2bf99bdcb89bf852",
"5c1e74518dd70e4f1506b4f64da7b5f3"
"5c1e74518dd70e4f1506b4f64da7b5f3",
[
"versions.yml:md5,32dd6a2d25ace29928423400082ed21e",
"versions.yml:md5,4f417b1f2243b8fdbb4d500d297275d7",
"versions.yml:md5,62a1dcf235b26d36556128000350f873",
"versions.yml:md5,65b00c07a75fb33c090cfdc3caf6c670",
"versions.yml:md5,703785e3662b35a0d9e533f0047fee5c",
"versions.yml:md5,7da162ffef1721b87e11194d10acaeee",
"versions.yml:md5,916a9eda18796248d67f0775546401a1",
"versions.yml:md5,9c1eaf84889a0aa32a7e224bb59cc614",
"versions.yml:md5,e22c32ec91f95bda4130664671ca7cea"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.10.0"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-11-28T11:03:31.491281"
"timestamp": "2025-12-10T15:09:04.590361686"
}
}
6 changes: 6 additions & 0 deletions subworkflows/nf-core/fastq_remove_rrna/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,7 @@ nextflow_workflow {
{ assert pelines2.size() == 16636 },
{ assert sortmernaRrnaCount == 20 }, // 10 pairs = 20 individual reads (100% detection)
{ assert snapshot(
workflow.out.versions,
pelines1.join('\n').md5(),
pelines2.join('\n').md5()
).match() }
Expand Down Expand Up @@ -126,6 +127,7 @@ nextflow_workflow {
{ assert pelines2.size() == 16648 },
{ assert ribodetectorRrnaCount == 7 }, // 7 pairs detected (70% - ML model misses some)
{ assert snapshot(
workflow.out.versions,
sortedLines1.join('\n').md5(),
sortedLines2.join('\n').md5()
).match() }
Expand Down Expand Up @@ -171,6 +173,7 @@ nextflow_workflow {
{ assert pelines2.size() == 16636 },
{ assert bowtie2RrnaCount == 17 }, // 17 mates aligned to rRNA reference
{ assert snapshot(
workflow.out.versions,
pelines1.join('\n').md5(),
pelines2.join('\n').md5()
).match() }
Expand Down Expand Up @@ -233,6 +236,7 @@ nextflow_workflow {
{ assert selines.size() == 16636 }, // 4159 reads × 4 lines/read
{ assert bowtie2RrnaCount == 10 }, // 10 reads aligned to rRNA reference
{ assert snapshot(
workflow.out.versions,
selines.join('\n').md5()
).match() }
)
Expand Down Expand Up @@ -290,6 +294,7 @@ nextflow_workflow {
{ assert selines.size() == 16636 }, // 4159 reads × 4 lines/read
{ assert sortmernaRrnaCount == 10 }, // 10 reads detected (100% detection)
{ assert snapshot(
workflow.out.versions,
selines.join('\n').md5()
).match() }
)
Expand Down Expand Up @@ -333,6 +338,7 @@ nextflow_workflow {
// even when the same rRNA databases are provided multiple times
assertAll(
{ assert workflow.success },
{ assert snapshot(workflow.out.versions).match() },
{ assert pelines1.size() >= 0 }, // Should have some reads
{ assert pelines2.size() >= 0 }, // Should have some reads
{ assert !workflow.stderr.contains("Duplicate entry") }, // No duplicate header errors in stderr
Expand Down
60 changes: 50 additions & 10 deletions subworkflows/nf-core/fastq_remove_rrna/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,55 +1,95 @@
{
"homo_sapiens single-end [fastq] bowtie2": {
"content": [
[
"versions.yml:md5,2cfbbdad4c4dcdfacedeb20ec188145b",
"versions.yml:md5,5edeace71a857688bae03f7a5c102caf",
"versions.yml:md5,98dd18ffc97251b8a24e611b27ba12af",
"versions.yml:md5,cb634680924d1a6f4c7de81a23a2e992"
],
"bdea4e3bbdbb7c301ff578b9d8976fb6"
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-11-28T11:51:37.291482561"
"timestamp": "2025-12-10T15:48:50.273951118"
},
"homo_sapiens single-end [fastq] sortmerna": {
"content": [
[
"versions.yml:md5,d375aebf400213ebbd6e104a331b27ae"
],
"bdea4e3bbdbb7c301ff578b9d8976fb6"
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-11-28T11:51:50.835424985"
"timestamp": "2025-12-10T15:49:01.125046076"
},
"homo_sapiens paired-end [fastq] bowtie2 with duplicate rrna databases": {
"content": [
[
"versions.yml:md5,2cfbbdad4c4dcdfacedeb20ec188145b",
"versions.yml:md5,2cfbbdad4c4dcdfacedeb20ec188145b",
"versions.yml:md5,5edeace71a857688bae03f7a5c102caf",
"versions.yml:md5,5edeace71a857688bae03f7a5c102caf",
"versions.yml:md5,98dd18ffc97251b8a24e611b27ba12af",
"versions.yml:md5,a9810676328a1650fc826978ae8eb96b",
"versions.yml:md5,bee00b6ec637b583decca8bd9c9eacd0"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-12-10T15:49:36.940527491"
},
"homo_sapiens paired-end [fastq] sortmerna": {
"content": [
[
"versions.yml:md5,d375aebf400213ebbd6e104a331b27ae"
],
"bdea4e3bbdbb7c301ff578b9d8976fb6",
"1b83618177abebeb38c29d2258efdd4f"
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-11-28T11:49:53.980824473"
"timestamp": "2025-12-10T15:48:17.279619846"
},
"homo_sapiens paired-end [fastq] ribodetector": {
"content": [
[
"versions.yml:md5,acaf2e83db2526761adf39c912b0037c"
],
"ec0260bcdeef6af8a9b6d470eafb5603",
"a0ef8564218df5741dee81f03db13600"
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-11-29T18:27:41.89909077"
"timestamp": "2025-12-10T15:48:30.322253019"
},
"homo_sapiens paired-end [fastq] bowtie2": {
"content": [
[
"versions.yml:md5,2cfbbdad4c4dcdfacedeb20ec188145b",
"versions.yml:md5,5edeace71a857688bae03f7a5c102caf",
"versions.yml:md5,98dd18ffc97251b8a24e611b27ba12af",
"versions.yml:md5,a9810676328a1650fc826978ae8eb96b",
"versions.yml:md5,bee00b6ec637b583decca8bd9c9eacd0"
],
"4ef4e259208497288aaefaa88770975d",
"63198a2af4a4a8fb949b01a8b2c4cb7c"
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-11-28T11:51:24.742227098"
"timestamp": "2025-12-10T15:48:40.498006186"
}
}
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