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Merge pull request #487 from nf-core/fix-nf-test-version
Fix nf test version
2 parents 8bd9308 + 59de85c commit 22a4cb3

13 files changed

+45
-66
lines changed

‎nf-test.config‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,6 +19,6 @@ config {
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// load the necessary plugins
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plugins {
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load "[email protected].3"
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load "[email protected].5"
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}
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}

‎tests/main_pipeline_cellranger.nf.test‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@ nextflow_pipeline {
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
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removeNextflowVersion("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml"),
27+
removeFromYamlMap("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", "Workflow"),
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// All stable path name, with a relative path
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stable_name,
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// All files with stable contents

‎tests/main_pipeline_cellranger.nf.test.snap‎

Lines changed: 5 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -16,13 +16,10 @@
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"fastqc": "0.12.1"
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},
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"MTX_TO_H5AD": {
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"python": "3.12.5",
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"scanpy": "1.10.2",
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"anndata": "0.10.8",
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"pandas": "2.2.2",
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"anndata": "0.10.8"
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},
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"Workflow": {
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"nf-core/scrnaseq": "v4.1.0dev"
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"python": "3.12.5",
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"scanpy": "1.10.2"
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}
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},
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[
@@ -383,8 +380,8 @@
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.1"
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-08-01T11:05:37.982319489"
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"timestamp": "2025-08-04T08:28:33.037302748"
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}
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}

‎tests/main_pipeline_cellrangerarc.nf.test‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,7 @@ nextflow_pipeline {
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
32-
removeNextflowVersion("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml"),
32+
removeFromYamlMap("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", "Workflow"),
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// All stable path name, with a relative path
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stable_name,
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// All files with stable contents

‎tests/main_pipeline_cellrangerarc.nf.test.snap‎

Lines changed: 5 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -16,13 +16,10 @@
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"fastqc": "0.12.1"
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},
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"MTX_TO_H5AD": {
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"python": "3.12.5",
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"scanpy": "1.10.2",
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"anndata": "0.10.8",
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"pandas": "2.2.2",
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"anndata": "0.10.8"
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},
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"Workflow": {
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"nf-core/scrnaseq": "v4.1.0dev"
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"python": "3.12.5",
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"scanpy": "1.10.2"
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}
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},
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[
@@ -286,8 +283,8 @@
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.1"
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-08-01T11:18:19.395555812"
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"timestamp": "2025-08-04T08:33:34.787444894"
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}
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}

‎tests/main_pipeline_cellrangermulti.nf.test‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,7 @@ nextflow_pipeline {
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
38-
removeNextflowVersion("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml"),
38+
removeFromYamlMap("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", "Workflow"),
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// All stable path name, with a relative path
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stable_name,
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// All files with stable contents
@@ -73,7 +73,7 @@ nextflow_pipeline {
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
76-
removeNextflowVersion("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml"),
76+
removeFromYamlMap("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", "Workflow"),
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// All stable path name, with a relative path
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stable_name,
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// All files with stable contents

‎tests/main_pipeline_cellrangermulti.nf.test.snap‎

Lines changed: 10 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -25,13 +25,10 @@
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"gunzip": 1.1
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},
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"MTX_TO_H5AD": {
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"python": "3.12.5",
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"scanpy": "1.10.2",
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"anndata": "0.10.8",
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"pandas": "2.2.2",
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"anndata": "0.10.8"
32-
},
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"Workflow": {
34-
"nf-core/scrnaseq": "v4.1.0dev"
30+
"python": "3.12.5",
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"scanpy": "1.10.2"
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}
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},
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[
@@ -1247,9 +1244,9 @@
12471244
],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.1"
1247+
"nextflow": "25.04.6"
12511248
},
1252-
"timestamp": "2025-08-01T11:43:41.46111504"
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"timestamp": "2025-08-04T08:47:14.585663687"
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},
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"test-dataset_cellrangermulti_aligner_rat": {
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"content": [
@@ -1277,13 +1274,10 @@
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"gunzip": 1.1
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},
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"MTX_TO_H5AD": {
1280-
"python": "3.12.5",
1281-
"scanpy": "1.10.2",
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"anndata": "0.10.8",
12821278
"pandas": "2.2.2",
1283-
"anndata": "0.10.8"
1284-
},
1285-
"Workflow": {
1286-
"nf-core/scrnaseq": "v4.1.0dev"
1279+
"python": "3.12.5",
1280+
"scanpy": "1.10.2"
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}
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},
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[
@@ -1854,8 +1848,8 @@
18541848
],
18551849
"meta": {
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"nf-test": "0.9.2",
1857-
"nextflow": "24.10.1"
1851+
"nextflow": "25.04.6"
18581852
},
1859-
"timestamp": "2025-08-01T12:02:57.754836314"
1853+
"timestamp": "2025-08-04T08:56:26.746631285"
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}
18611855
}

‎tests/main_pipeline_kallisto.nf.test‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@ nextflow_pipeline {
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// Number of successful tasks
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workflow.trace.succeeded().size(),
2626
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
27-
removeNextflowVersion("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml"),
27+
removeFromYamlMap("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", "Workflow"),
2828
// All stable path name, with a relative path
2929
stable_name,
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// All files with stable contents

‎tests/main_pipeline_kallisto.nf.test.snap‎

Lines changed: 5 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -13,13 +13,10 @@
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"kallistobustools": "0.28.2"
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},
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"MTX_TO_H5AD": {
16-
"python": "3.12.5",
17-
"scanpy": "1.10.2",
16+
"anndata": "0.10.8",
1817
"pandas": "2.2.2",
19-
"anndata": "0.10.8"
20-
},
21-
"Workflow": {
22-
"nf-core/scrnaseq": "v4.1.0dev"
18+
"python": "3.12.5",
19+
"scanpy": "1.10.2"
2320
}
2421
},
2522
[
@@ -212,8 +209,8 @@
212209
],
213210
"meta": {
214211
"nf-test": "0.9.2",
215-
"nextflow": "24.10.1"
212+
"nextflow": "25.04.6"
216213
},
217-
"timestamp": "2025-08-01T12:08:34.446984853"
214+
"timestamp": "2025-08-04T09:00:22.183689983"
218215
}
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}

‎tests/main_pipeline_simpleaf.nf.test‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@ nextflow_pipeline {
2424
// Number of successful tasks
2525
workflow.trace.succeeded().size(),
2626
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
27-
removeNextflowVersion("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml"),
27+
removeFromYamlMap("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", "Workflow"),
2828
// All stable path name, with a relative path
2929
stable_name,
3030
// All files with stable contents

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