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SusiJoSusiJo
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update tests
1 parent 6b720d6 commit 4b489d6

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Lines changed: 1335 additions & 574 deletions

‎tests/.nftignore‎

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@@ -13,3 +13,7 @@ shinyngs_app/**/data.rds
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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.results.tsv
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**/**/*.dream.results.tsv
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**/**/*.limma.results.tsv
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**/**/*.limma.results_filtered.tsv

‎tests/test_affy.nf.test‎

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@@ -5,7 +5,7 @@ nextflow_pipeline {
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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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‎tests/test_affy.nf.test.snap‎

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@@ -267,8 +267,6 @@
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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",
@@ -283,7 +281,7 @@
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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": "2025-06-17T13:47:55.740801939"
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},
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"Test affy profile - with toolsheet": {
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"content": [
@@ -553,8 +551,6 @@
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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": "2025-06-17T13:51:07.757386695"
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}
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}

‎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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‎tests/test_maxquant.nf.test.snap‎

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@@ -29,6 +29,33 @@
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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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"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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"PROTEUS": {
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"r-base": "4.2.1",
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"r-proteus-bartongroup": "0.2.16",
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"r-plotly": "4.10.2",
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"bioconductor-limma": "3.54.0"
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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/limma",
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"raw_proteingroups.rds:md5,daef7d25977a1628870dee75e2977ee3",
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"versions.yml:md5,225ced8832439345efa781c726cf2e5c",
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"versions.yml:md5,d5f6ad8fe6242dcd75bc62b654d1d211",
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"fakebatch_fakeBatch_b1_b2_PXD043349.limma.results.tsv:md5,8cdd17fbb6ab065811ed775849f4218a",
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"fakebatch_fakeBatch_b1_b2_PXD043349.limma.results_filtered.tsv:md5,50d7e7ece68f799b73333ccd6a159078",
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"genotype_celltype_t1_FoB_PXD043349.limma.results.tsv:md5,f5c222dbc6202e7222edcbdd9be9b138",
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"genotype_celltype_t1_FoB_PXD043349.limma.results_filtered.tsv:md5,50dc06d421f7d51f2ef0f45ebc9d5671",
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"genotype_celltype_t1_MZ_fakeBatch_PXD043349.limma.results.tsv:md5,3e68964f1f43965890602cca8de3ea24",
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"genotype_celltype_t1_MZ_fakeBatch_PXD043349.limma.results_filtered.tsv:md5,664e6cb3fad5744724e2736749ce1357",
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"genotype_celltype_t1_t2_PXD043349.limma.results.tsv:md5,46fb6997ad46f3c8ae9044d76e4dcb99",
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"genotype_celltype_t1_t2_PXD043349.limma.results_filtered.tsv:md5,cdd22b242d8fe1e7ace48d8c73a66b25",
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"normalizeMedian.normalized_proteingroups_tab.tsv:md5,154fcd8d23409981b897d153e7b7e34e",
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"raw_proteingroups_tab.tsv:md5,33a8791f84c676ea1aea4842231acb6a",
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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": "2025-06-17T13:00:28.84951094"
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"timestamp": "2025-06-17T13:25:15.519554825"
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},
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"Test maxquant 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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"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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"PROTEUS": {
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"r-base": "4.2.1",
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"r-proteus-bartongroup": "0.2.16",
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"r-plotly": "4.10.2",
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"bioconductor-limma": "3.54.0"
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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/limma",
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"raw_proteingroups.rds:md5,daef7d25977a1628870dee75e2977ee3",
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"versions.yml:md5,225ced8832439345efa781c726cf2e5c",
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"versions.yml:md5,d5f6ad8fe6242dcd75bc62b654d1d211",
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"fakebatch_fakeBatch_b1_b2_PXD043349.limma.results.tsv:md5,8cdd17fbb6ab065811ed775849f4218a",
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"fakebatch_fakeBatch_b1_b2_PXD043349.limma.results_filtered.tsv:md5,50d7e7ece68f799b73333ccd6a159078",
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"genotype_celltype_t1_FoB_PXD043349.limma.results.tsv:md5,f5c222dbc6202e7222edcbdd9be9b138",
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"genotype_celltype_t1_FoB_PXD043349.limma.results_filtered.tsv:md5,50dc06d421f7d51f2ef0f45ebc9d5671",
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"genotype_celltype_t1_MZ_fakeBatch_PXD043349.limma.results.tsv:md5,3e68964f1f43965890602cca8de3ea24",
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"genotype_celltype_t1_MZ_fakeBatch_PXD043349.limma.results_filtered.tsv:md5,664e6cb3fad5744724e2736749ce1357",
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"genotype_celltype_t1_t2_PXD043349.limma.results.tsv:md5,46fb6997ad46f3c8ae9044d76e4dcb99",
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"genotype_celltype_t1_t2_PXD043349.limma.results_filtered.tsv:md5,cdd22b242d8fe1e7ace48d8c73a66b25",
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"normalizeMedian.normalized_proteingroups_tab.tsv:md5,154fcd8d23409981b897d153e7b7e34e",
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"raw_proteingroups_tab.tsv:md5,33a8791f84c676ea1aea4842231acb6a",
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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": "2025-06-17T13:01:31.502573937"
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"timestamp": "2025-06-17T13:26:18.176770325"
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}
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}

tests/test_nogtf.nf.test.bak renamed to tests/test_nogtf.nf.test

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@@ -5,37 +5,12 @@ nextflow_pipeline {
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tag "nogtf"
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tag "pipeline"
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profile "test_nogtf"
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config "../conf/rnaseq.config"
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test("Test no gtf profile") {
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when {
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params {
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outdir = "$outputDir"
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study_name = 'SRP254919'
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config_profile_name = 'Test nogtf profile'
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config_profile_description = 'Minimal test dataset to check pipeline function'
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// Input data
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv'
21-
matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv'
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contrasts_yml = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/testdata/SRP254919.contrasts.yaml'
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//Features
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features_metadata_cols = 'gene_id,gene_name'
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// Observations
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observations_id_col = 'sample'
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observations_name_col = 'sample'
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// Apply a higher filter to check that the filtering works
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filtering_min_abundance = 10
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// Exploratory
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exploratory_main_variable = 'contrasts'
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// Test dataset is too small for the nsub default value
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deseq2_vst_nsub = 500
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}
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}
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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"),
29+
removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
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// All stable path name, with a relative path
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stable_name,
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// All files with stable contents
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outdir = "$outputDir"
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paramset_name = "deseq2_rnaseq"
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differential_method = null
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study_name = 'SRP254919'
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config_profile_name = 'Test nogtf profile - with toolsheet'
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config_profile_description = 'Minimal test dataset to check pipeline function'
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// Input data
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv'
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matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv'
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contrasts_yml = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/testdata/SRP254919.contrasts.yaml'
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//Features
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features_metadata_cols = 'gene_id,gene_name'
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// Observations
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observations_id_col = 'sample'
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observations_name_col = 'sample'
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// Apply a higher filter to check that the filtering works
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filtering_min_abundance = 10
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// Exploratory
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exploratory_main_variable = 'contrasts'
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// Test dataset is too small for the nsub default value
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deseq2_vst_nsub = 500
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}
9647
}
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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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