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update tests
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lines changed

‎tests/.nftignore‎

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@@ -12,4 +12,9 @@ shinyngs_app/**/data.rds
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.DS_Store
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*.dds.rld.rds
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**/**/*.dds.rld.rds
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*.limma.rds
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**/**/*.limma.rds
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*.results.tsv
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*.results_filtered.tsv
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**/**/*.results.tsv
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**/**/*.results_filtered.tsv

‎tests/default.nf.test‎

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@@ -29,7 +29,6 @@ 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 tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"),
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
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// All stable path name, with a relative path
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stable_name,
@@ -63,7 +62,6 @@ 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 tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"),
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
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// All stable path name, with a relative path
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stable_name,

‎tests/default.nf.test.snap‎

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@@ -51,55 +51,6 @@
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"nf-core/differentialabundance": "v1.6.0dev"
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}
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},
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{
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"CUSTOM_FILTERDIFFERENTIALTABLE": {
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"pandas": "1.5.2"
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},
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"CUSTOM_TABULARTOGSEACHIP": {
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"gawk": "5.1.0"
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},
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"CUSTOM_TABULARTOGSEACLS": {
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"awk": "1.3.4"
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},
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"CUSTOM_TABULARTOGSEAGCT": {
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"awk": "1.3.4"
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},
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"DESEQ2_DIFFERENTIAL": {
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"r-base": "4.1.3",
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"bioconductor-deseq2": "1.34.0"
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},
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"DESEQ2_NORM": {
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"r-base": "4.1.3",
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"bioconductor-deseq2": "1.34.0"
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},
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"GSEA_GSEA": {
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"gsea": "4.3.2"
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},
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"GTF_TO_TABLE": {
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"atlas-gene-annotation-manipulation": "1.1.1"
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},
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"GUNZIP_GTF": {
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"gunzip": 1.1
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},
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"IMMUNEDECONV": {
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"r-immunedeconv": "2.1.0"
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},
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"PLOT_DIFFERENTIAL": {
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"r-shinyngs": "2.2.4"
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},
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"PLOT_EXPLORATORY": {
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"r-shinyngs": "2.2.4"
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},
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"SHINYNGS_APP": {
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"r-shinyngs": "2.2.4"
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},
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"VALIDATOR": {
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"r-shinyngs": "2.2.4"
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},
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"Workflow": {
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"nf-core/differentialabundance": "v1.6.0dev"
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}
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},
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[
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"other",
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"other/deseq2",
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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},
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"timestamp": "2025-06-16T14:51:47.428621925"
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"timestamp": "2025-06-17T15:12:35.519718769"
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},
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"Test profile - with toolsheet": {
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"content": [
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"nf-core/differentialabundance": "v1.6.0dev"
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}
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},
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{
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"CUSTOM_FILTERDIFFERENTIALTABLE": {
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"pandas": "1.5.2"
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},
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"CUSTOM_TABULARTOGSEACHIP": {
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"gawk": "5.1.0"
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},
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"CUSTOM_TABULARTOGSEACLS": {
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"awk": "1.3.4"
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},
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"CUSTOM_TABULARTOGSEAGCT": {
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"awk": "1.3.4"
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},
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"DESEQ2_DIFFERENTIAL": {
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"r-base": "4.1.3",
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"bioconductor-deseq2": "1.34.0"
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},
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"DESEQ2_NORM": {
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"r-base": "4.1.3",
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"bioconductor-deseq2": "1.34.0"
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},
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"GSEA_GSEA": {
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"gsea": "4.3.2"
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},
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"GTF_TO_TABLE": {
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"atlas-gene-annotation-manipulation": "1.1.1"
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},
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"GUNZIP_GTF": {
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"gunzip": 1.1
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},
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"IMMUNEDECONV": {
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"r-immunedeconv": "2.1.0"
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},
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"PLOT_DIFFERENTIAL": {
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"r-shinyngs": "2.2.4"
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},
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"PLOT_EXPLORATORY": {
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"r-shinyngs": "2.2.4"
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},
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"SHINYNGS_APP": {
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"r-shinyngs": "2.2.4"
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},
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"VALIDATOR": {
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"r-shinyngs": "2.2.4"
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},
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"Workflow": {
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"nf-core/differentialabundance": "v1.6.0dev"
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}
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},
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[
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"other",
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"other/deseq2",
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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},
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"timestamp": "2025-06-16T14:50:27.028192334"
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"timestamp": "2025-06-17T15:11:12.568576871"
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},
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"Test profile - yml no formula": {
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"content": [

‎tests/test_affy.nf.test‎

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@@ -4,8 +4,7 @@ nextflow_pipeline {
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script "../main.nf"
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tag "affy"
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tag "pipeline"
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config "../conf/affy.config"
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profile "test_affy,affy"
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profile "test_affy"
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test("Test affy profile") {
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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 tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"),
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
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// All stable path name, with a relative path
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stable_name,
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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 tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"),
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
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// All stable path name, with a relative path
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stable_name,

‎tests/test_affy.nf.test.snap‎

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@@ -42,46 +42,6 @@
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"nf-core/differentialabundance": "v1.6.0dev"
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}
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},
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{
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"AFFY_JUSTRMA_RAW": {
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"r-base": "4.3.1",
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"bioconductor-affy": "1.78.0"
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},
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"CUSTOM_FILTERDIFFERENTIALTABLE": {
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"pandas": "1.5.2"
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},
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"CUSTOM_TABULARTOGSEACHIP": {
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"gawk": "5.1.0"
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},
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"CUSTOM_TABULARTOGSEACLS": {
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"awk": "1.3.4"
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},
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"CUSTOM_TABULARTOGSEAGCT": {
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"awk": "1.3.4"
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},
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"GSEA_GSEA": {
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"gsea": "4.3.2"
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},
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"LIMMA_DIFFERENTIAL": {
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"r-base": "4.3.3",
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"bioconductor-limma": "3.58.1"
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},
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"PLOT_DIFFERENTIAL": {
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"r-shinyngs": "2.2.4"
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},
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"PLOT_EXPLORATORY": {
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"r-shinyngs": "2.2.4"
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},
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"SHINYNGS_APP": {
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"r-shinyngs": "2.2.4"
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},
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"VALIDATOR": {
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"r-shinyngs": "2.2.4"
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},
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"Workflow": {
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"nf-core/differentialabundance": "v1.6.0dev"
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}
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},
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[
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"other",
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"other/affy",
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"app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
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"versions.yml:md5,b3436c10ff83d0dab55060de3cae3ef2",
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"hgu133plus2.annotation.tsv:md5,f2b82ef12b2a2e8e575de06766583d96",
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"phenotype_uninvolved_lesional_GSE50790.limma.results.tsv:md5,91bfc5e94dd232b927c3fc7f3ece7e36",
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"phenotype_uninvolved_lesional_GSE50790.limma.results_filtered.tsv:md5,445b8fd9dcd34c2d273613b03ead0a7f",
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"GSM1229341_Gudjohnsson_001_6690_PP.CEL.gz:md5,259d0908211a071351450f366fd51cad",
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"GSM1229342_Gudjohnsson_002_6690_PN.CEL.gz:md5,31cc2b8b26e210760b8ebd4b304b52ba",
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"GSM1229343_Gudjohnsson_003_7450_PN.CEL.gz:md5,713a3ca75a883cbff6da0be7bd251422",
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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},
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"timestamp": "2025-06-17T09:35:13.777853554"
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"timestamp": "2025-06-17T15:17:08.723393528"
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},
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"Test affy profile - with toolsheet": {
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"content": [
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"nf-core/differentialabundance": "v1.6.0dev"
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}
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},
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{
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"AFFY_JUSTRMA_RAW": {
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"r-base": "4.3.1",
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"bioconductor-affy": "1.78.0"
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},
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"CUSTOM_FILTERDIFFERENTIALTABLE": {
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"pandas": "1.5.2"
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},
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"CUSTOM_TABULARTOGSEACHIP": {
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"gawk": "5.1.0"
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},
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"CUSTOM_TABULARTOGSEACLS": {
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"awk": "1.3.4"
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},
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"CUSTOM_TABULARTOGSEAGCT": {
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"awk": "1.3.4"
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},
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"GSEA_GSEA": {
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"gsea": "4.3.2"
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},
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"LIMMA_DIFFERENTIAL": {
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"r-base": "4.3.3",
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"bioconductor-limma": "3.58.1"
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},
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"PLOT_DIFFERENTIAL": {
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"r-shinyngs": "2.2.4"
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},
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"PLOT_EXPLORATORY": {
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"r-shinyngs": "2.2.4"
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},
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"SHINYNGS_APP": {
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"r-shinyngs": "2.2.4"
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},
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"VALIDATOR": {
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"r-shinyngs": "2.2.4"
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},
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"Workflow": {
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"nf-core/differentialabundance": "v1.6.0dev"
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}
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},
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[
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"other",
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"other/affy",
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"app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
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"versions.yml:md5,b3436c10ff83d0dab55060de3cae3ef2",
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"hgu133plus2.annotation.tsv:md5,f2b82ef12b2a2e8e575de06766583d96",
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"phenotype_uninvolved_lesional_GSE50790.limma.results.tsv:md5,91bfc5e94dd232b927c3fc7f3ece7e36",
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"phenotype_uninvolved_lesional_GSE50790.limma.results_filtered.tsv:md5,445b8fd9dcd34c2d273613b03ead0a7f",
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"GSM1229341_Gudjohnsson_001_6690_PP.CEL.gz:md5,259d0908211a071351450f366fd51cad",
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"GSM1229342_Gudjohnsson_002_6690_PN.CEL.gz:md5,31cc2b8b26e210760b8ebd4b304b52ba",
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"GSM1229343_Gudjohnsson_003_7450_PN.CEL.gz:md5,713a3ca75a883cbff6da0be7bd251422",
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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},
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"timestamp": "2025-06-17T09:38:26.821359936"
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"timestamp": "2025-06-17T15:20:21.3699015"
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}
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}

‎tests/test_custom_paramsheet.nf.test‎

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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 tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"),
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
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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
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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 tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"),
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
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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/test_maxquant.nf.test‎

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@@ -4,7 +4,7 @@ nextflow_pipeline {
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script "../main.nf"
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tag "maxquant"
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tag "pipeline"
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profile "test_maxquant,maxquant"
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profile "test_maxquant"
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test("Test maxquant profile") {
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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 tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"),
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
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// All stable path name, with a relative path
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stable_name,
@@ -62,7 +61,6 @@ 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 tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"),
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
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// All stable path name, with a relative path
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stable_name,

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