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Nft utils tuple match warn #1986

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0f51f2c
add no tuple warning check
maxulysse Sep 17, 2025
24384cd
Catch all tuple mismatch warning
maxulysse Sep 17, 2025
06c339d
update CHANGELOG
maxulysse Sep 17, 2025
0a02b90
Capture warnings
maxulysse Sep 17, 2025
2851650
Merge branch 'dev' into nft-utils_tuple-match-warn
maxulysse Sep 17, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -105,6 +105,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [1835](https://github.com/nf-core/sarek/pull/1835) - Add GPU testing possibilities
- [1855](https://github.com/nf-core/sarek/pull/1855) - Add contributors info to the contributors field in the manifest
- [1922](https://github.com/nf-core/sarek/pull/1922) - Added tests for ASCAT
- [1986](https://github.com/nf-core/sarek/pull/1986) - Added checks for tuple mismatch warnings

#### Changed

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2 changes: 1 addition & 1 deletion nf-test.config
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Expand Up @@ -20,7 +20,7 @@ config {
// load the necessary plugins
plugins {
load "[email protected]"
load "[email protected].5"
load "[email protected].6"
load "[email protected]"
}
}
12 changes: 8 additions & 4 deletions tests/aligner-bwa-mem.nf.test.snap
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Expand Up @@ -70,7 +70,8 @@
[
"test.sorted.cram:md5,5534c350547fd253f0f2b9450362bed"
],
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -114,7 +115,8 @@
"reference/intervals/genome.bed.gz",
"reference/intervals/genome.stub.bed",
"reference/intervals/genome.stub.bed.gz"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -172,7 +174,8 @@
],
"No BAM files",
"No CRAM files",
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -235,7 +238,8 @@
"reference/intervals/genome.bed.gz",
"reference/intervals/genome.stub.bed",
"reference/intervals/genome.stub.bed.gz"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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6 changes: 4 additions & 2 deletions tests/aligner-bwa-mem2.nf.test.snap
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Expand Up @@ -49,7 +49,8 @@
],
"No BAM files",
"No CRAM files",
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -128,7 +129,8 @@
[
"test.sorted.cram:md5,5534c350547fd253f0f2b9450362bed"
],
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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6 changes: 4 additions & 2 deletions tests/aligner-dragmap.nf.test.snap
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Expand Up @@ -52,7 +52,8 @@
],
"No BAM files",
"No CRAM files",
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -135,7 +136,8 @@
[
"test.sorted.cram:md5,7088dc71e5390aec0dd9d778f4568297"
],
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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6 changes: 4 additions & 2 deletions tests/aligner-parabricks.nf.test.snap
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Expand Up @@ -206,7 +206,8 @@
"test-test_L1.cram:md5,56ead4e3efd69b35a8e539b1b697213d",
"test-test_L2.cram:md5,56ead4e3efd69b35a8e539b1b697213d"
],
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -507,7 +508,8 @@
[
"test2_vs_test.mutect2.filtered.vcf.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
"test2_vs_test.mutect2.vcf.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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3 changes: 2 additions & 1 deletion tests/alignment_from_everything.nf.test.snap
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Expand Up @@ -430,7 +430,8 @@
"test_bam.recal.bam:md5,95a95d43e1db35c58b311dee4338c05b"
],
"No CRAM files",
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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3 changes: 2 additions & 1 deletion tests/alignment_to_fastq.nf.test.snap
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Expand Up @@ -281,7 +281,8 @@
"test.recal.bam:md5,95a95d43e1db35c58b311dee4338c05b"
],
"No CRAM files",
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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3 changes: 2 additions & 1 deletion tests/annotation_bcfann.nf.test.snap
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Expand Up @@ -33,7 +33,8 @@
"No CRAM files",
[
"test_BCF.ann.vcf.gz:md5,bc7bf3ee9e8430e064c539eb81e59bf9"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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6 changes: 4 additions & 2 deletions tests/annotation_merge.nf.test.snap
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Expand Up @@ -101,7 +101,8 @@
"test_VEP.ann.vcf.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_snpEff.ann.vcf.gz:md5,fd266e623365c7d1837bc9eb088fe70c",
"test_snpEff_VEP.ann.vcf.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -200,7 +201,8 @@
"No CRAM files",
[
"test_snpEff_VEP.ann.vcf.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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8 changes: 5 additions & 3 deletions tests/default.nf.test.snap
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Expand Up @@ -282,7 +282,8 @@
[
"test.strelka.genome.vcf.gz:md5,16437a040679d88b7d84a9276f793d6c",
"test.strelka.variants.vcf.gz:md5,666f835fdaf4952a179cdedd40c9d565"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -487,12 +488,13 @@
"variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi",
"variant_calling/strelka/test/test.strelka.variants.vcf.gz",
"variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-07-11T10:26:03.957093162"
"timestamp": "2025-09-17T09:41:38.503793146"
}
}
6 changes: 4 additions & 2 deletions tests/fastp.nf.test.snap
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Expand Up @@ -341,7 +341,8 @@
"test.md.cram:md5,9a65845bff32f674fd01e736743dd4b5",
"test.recal.cram:md5,6730f24d62a7bc9aa1e9fb0f89ae9cde"
],
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -715,7 +716,8 @@
"test.md.cram:md5,109bcdc3a3c2720d46cb85268920f85c",
"test.recal.cram:md5,f89c35bd0e96b2254e36b4e3660b1269"
],
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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18 changes: 12 additions & 6 deletions tests/intervals.nf.test.snap
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Expand Up @@ -71,7 +71,8 @@
[
"test.sorted.cram:md5,5534c350547fd253f0f2b9450362bed"
],
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -126,7 +127,8 @@
[
"test.sorted.cram:md5,5534c350547fd253f0f2b9450362bed"
],
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -178,7 +180,8 @@
[
"test.sorted.cram:md5,5534c350547fd253f0f2b9450362bed"
],
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -224,7 +227,8 @@
"preprocessing/mapped/test/test.sorted.cram",
"preprocessing/mapped/test/test.sorted.cram.crai",
"reference"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -288,7 +292,8 @@
"reference/intervals/fai.bed.gz",
"reference/intervals/fai.stub.bed",
"reference/intervals/fai.stub.bed.gz"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -337,7 +342,8 @@
"preprocessing/mapped/test/test.sorted.cram",
"preprocessing/mapped/test/test.sorted.cram.crai",
"reference"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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6 changes: 4 additions & 2 deletions tests/joint_calling_haplotypecaller.nf.test.snap
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Expand Up @@ -203,7 +203,8 @@
"joint_germline.vcf.gz:md5,3551d1de0abc899d2bbd0cbe1336f832",
"testN.haplotypecaller.g.vcf.gz:md5,44590f25a9ed621929879cefc601f95a",
"testT.haplotypecaller.g.vcf.gz:md5,e37d210dda0bfe2716502353328b1103"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -412,7 +413,8 @@
"joint_germline.vcf.gz:md5,3551d1de0abc899d2bbd0cbe1336f832",
"testN.haplotypecaller.g.vcf.gz:md5,44590f25a9ed621929879cefc601f95a",
"testT.haplotypecaller.g.vcf.gz:md5,e37d210dda0bfe2716502353328b1103"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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6 changes: 4 additions & 2 deletions tests/joint_calling_mutect2.nf.test.snap
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Expand Up @@ -150,7 +150,8 @@
"No CRAM files",
[
"test.mutect2.vcf.gz:md5,593f6a3b49d8a4e44b1e2696883116c0"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -298,7 +299,8 @@
"No CRAM files",
[
"test.mutect2.vcf.gz:md5,e064ce0953bb07416f3bc8a60c761238"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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3 changes: 2 additions & 1 deletion tests/lane_integer.nf.test.snap
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Expand Up @@ -49,7 +49,8 @@
[
"test.sorted.cram:md5,5534c350547fd253f0f2b9450362bed"
],
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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3 changes: 2 additions & 1 deletion tests/lib/UTILS.groovy
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Expand Up @@ -128,7 +128,8 @@ class UTILS {
// Number of successful tasks
workflow.trace.succeeded().size(),
// All assertions based on the scenario
*UTILS.get_assertion(include_freebayes_unfiltered: scenario.include_freebayes_unfiltered ,include_muse_txt: scenario.include_muse_txt, no_vcf_md5sum: scenario.no_vcf_md5sum, outdir: params.outdir, stub: scenario.stub)
*UTILS.get_assertion(include_freebayes_unfiltered: scenario.include_freebayes_unfiltered ,include_muse_txt: scenario.include_muse_txt, no_vcf_md5sum: scenario.no_vcf_md5sum, outdir: params.outdir, stub: scenario.stub),
filterNextflowOutput(workflow.stdout + workflow.stderr, include: ["WARN"])?:"No warning"
).match() }
)
// Check stdout if specified
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3 changes: 2 additions & 1 deletion tests/postprocess_concatenation.nf.test.snap
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Expand Up @@ -281,7 +281,8 @@
"testN.haplotypecaller.vcf.gz:md5,9d9d103327d59d17e778b663b56136fb",
"testT.haplotypecaller.filtered.vcf.gz:md5,d1e2d43d91858677d2b35fc389ee81b1",
"testT.haplotypecaller.vcf.gz:md5,5a2f49f0a41e890f9564a0baa11dc1c6"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down
3 changes: 2 additions & 1 deletion tests/postprocess_concatenation_normalization.nf.test.snap
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Expand Up @@ -341,7 +341,8 @@
"testT.freebayes.norm.vcf.gz:md5,574d3d9e73986d07839d5e720c3ea929",
"testT.haplotypecaller.norm.vcf.gz:md5,9119ee2c970c37729dcb35d4b88f9d10",
"testT.vcf.gz:md5,9119ee2c970c37729dcb35d4b88f9d10"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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3 changes: 2 additions & 1 deletion tests/postprocess_normalization.nf.test.snap
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Expand Up @@ -297,7 +297,8 @@
"testT.freebayes.norm.vcf.gz:md5,574d3d9e73986d07839d5e720c3ea929",
"testT.haplotypecaller.norm.vcf.gz:md5,9119ee2c970c37729dcb35d4b88f9d10",
"testT.vcf.gz:md5,9119ee2c970c37729dcb35d4b88f9d10"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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6 changes: 4 additions & 2 deletions tests/qc_ngscheckmate.nf.test.snap
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Expand Up @@ -104,7 +104,8 @@
"reports/samtools/sample3/sample3.recal.cram.stats",
"reports/samtools/sample4",
"reports/samtools/sample4/sample4.recal.cram.stats"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down Expand Up @@ -268,7 +269,8 @@
"sample2.ngscheckmate.vcf.gz:md5,17c1253ed56084291e919586ecf9dca",
"sample3.ngscheckmate.vcf.gz:md5,5cffc2b460469247b346b2399dc016fd",
"sample4.ngscheckmate.vcf.gz:md5,17c1253ed56084291e919586ecf9dca"
]
],
"No warning"
],
"meta": {
"nf-test": "0.9.2",
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3 changes: 2 additions & 1 deletion tests/save_mapped.nf.test.snap
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Expand Up @@ -49,7 +49,8 @@
[
"test.sorted.cram:md5,5534c350547fd253f0f2b9450362bed"
],
"No VCF files"
"No VCF files",
"No warning"
],
"meta": {
"nf-test": "0.9.2",
Expand Down
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