From 8aa0e56cea203288a131483312af3142ee7c4afc Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Fri, 27 Dec 2024 19:18:27 +0000 Subject: [PATCH] Added nf-tests to gprofile2/gost --- modules/nf-core/gprofiler2/gost/main.nf | 24 ++- .../gost/templates/gprofiler2_gost.R | 2 +- .../gprofiler2/gost/tests/main.nf.test | 115 +++++++++++ .../gprofiler2/gost/tests/main.nf.test.snap | 193 ++++++++++++++++++ .../gprofiler2/gost/tests/nextflow.config | 3 + 5 files changed, 334 insertions(+), 3 deletions(-) create mode 100644 modules/nf-core/gprofiler2/gost/tests/main.nf.test create mode 100644 modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap create mode 100644 modules/nf-core/gprofiler2/gost/tests/nextflow.config diff --git a/modules/nf-core/gprofiler2/gost/main.nf b/modules/nf-core/gprofiler2/gost/main.nf index acb18b938ac..8428f514b74 100644 --- a/modules/nf-core/gprofiler2/gost/main.nf +++ b/modules/nf-core/gprofiler2/gost/main.nf @@ -4,8 +4,8 @@ process GPROFILER2_GOST { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-3712554873398d849d0d11b22440f41febbc4ede:aa19bb8afc0ec6456a4f3cd650f7577c3bbdd4f3-0': - 'biocontainers/mulled-v2-3712554873398d849d0d11b22440f41febbc4ede:aa19bb8afc0ec6456a4f3cd650f7577c3bbdd4f3-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e4b0e10a72db4ad519c128c4e3cef6e10bc1a83440af31f105ab389a5532589a/data': + 'community.wave.seqera.io/library/r-ggplot2_r-gprofiler2:fab855ea9f680400' }" input: tuple val(meta), path(de_file) @@ -28,4 +28,24 @@ process GPROFILER2_GOST { script: template 'gprofiler2_gost.R' + + stub: + def prefix = task.ext.prefix ?: meta.id + """ + touch ${prefix}.gprofiler2.all_enriched_pathways.tsv + touch ${prefix}.gprofiler2.gost_results.rds + touch ${prefix}.gprofiler2.gostplot.png + touch ${prefix}.gprofiler2.gostplot.html + touch ${prefix}.gprofiler2.*.sub_enriched_pathways.tsv + touch ${prefix}.gprofiler2.*.sub_enriched_pathways.png + touch ${prefix}.ENSG_filtered.gmt + touch ${prefix}.R_sessionInfo.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') + r-ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot2')))") + r-gprofiler2: \$(Rscript -e "library(gprofiler2); cat(as.character(packageVersion('gprofiler2')))") + END_VERSIONS + """ } diff --git a/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R b/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R index 1de2a754094..0e2c0f1e621 100644 --- a/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R +++ b/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R @@ -449,7 +449,7 @@ gprofiler2.version <- as.character(packageVersion('gprofiler2')) ggplot2.version <- as.character(packageVersion('ggplot2')) writeLines( c( - '"\${task.process}":', + '"$task.process":', paste(' r-base:', r.version), paste(' r-ggplot2:', ggplot2.version), paste(' r-gprofiler2:', gprofiler2.version) diff --git a/modules/nf-core/gprofiler2/gost/tests/main.nf.test b/modules/nf-core/gprofiler2/gost/tests/main.nf.test new file mode 100644 index 00000000000..fa8f94daf56 --- /dev/null +++ b/modules/nf-core/gprofiler2/gost/tests/main.nf.test @@ -0,0 +1,115 @@ +nextflow_process { + + name "Test Process GPROFILER2_GOST" + script "../main.nf" + process "GPROFILER2_GOST" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gprofiler" + tag "gprofiler_gost" + tag "gost" + tag "gprofiler2/gost" + tag "gprofiler2" + + test("test") { + + when { + params{ + gprofiler2_significant = true + gprofiler2_measure_underrepresentation = false + gprofiler2_correction_method = "gSCS" + gprofiler2_evcodes = false + gprofiler2_max_qval = 0.05 + gprofiler2_domain_scope = "annotated" + gprofiler2_min_diff = 1 + report_round_digits = 4 + gprofiler2_palette_name = "Blues" + differential_feature_id_column = "gene_id" + gprofiler2_token = null + gprofiler2_organism = "mmusculus" + gprofiler2_background_column = null + gprofiler2_sources = null + + module_args = [ + "--significant \"${params.gprofiler2_significant}\"", + "--measure_underrepresentation \"${params.gprofiler2_measure_underrepresentation}\"", + "--correction_method \"${params.gprofiler2_correction_method}\"", + "--evcodes \"${params.gprofiler2_evcodes}\"", + "--pval_threshold \"${params.gprofiler2_max_qval}\"", + "--domain_scope ${params.gprofiler2_domain_scope}", + "--min_diff \"${params.gprofiler2_min_diff}\"", + "--round_digits ${params.report_round_digits}", + "--palette_name \"${params.gprofiler2_palette_name}\"", + ((params.differential_feature_id_column == null) ? '' : "--de_id_column \"${params.differential_feature_id_column}\""), + ((params.gprofiler2_token == null) ? '' : "--token \"${params.gprofiler2_token}\""), + ((params.gprofiler2_organism == null) ? '' : "--organism \"${params.gprofiler2_organism}\""), + ((params.gprofiler2_background_column == null) ? '' : "--background_column \"${params.gprofiler2_background_column}\""), + ((params.gprofiler2_sources == null) ? '' : "--sources \"${params.gprofiler2_sources}\"") + ].join(' ').trim() + } + process { + """ + input[0] = [['id':'Condition_genotype_WT_KO', 'variable':'Condition genotype', 'reference':'WT', 'target':'KO', 'blocking':'batch'], file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/Condition_genotype_WT_KO.deseq2.results_filtered.tsv", checkIfExists: true)] + input[1] = file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/mus_musculus/gene_set_analysis/mh.all.v2022.1.Mm.symbols.gmt", checkIfExists: true) + input[2] = file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/study.filtered.tsv", checkIfExists: true) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.all_enrich, + process.out.plot_png, + process.out.sub_enrich, + process.out.sub_plot, + process.out.filtered_gmt, + process.out.session_info, + process.out.versions, + process.out.plot_html.collect{ meta,html -> file(html).name }, //assert unstable file + process.out.rds.collect{ meta,rds -> file(rds).name } //assert unstable file + ).match() + } + ) + } + } + + test("stub") { + + options "-stub" + + when { + params{ + module_args = null + } + process { + """ + input[0] = [['id':'Condition_genotype_WT_KO', 'variable':'Condition genotype', 'reference':'WT', 'target':'KO', 'blocking':'batch'], file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/Condition_genotype_WT_KO.deseq2.results_filtered.tsv", checkIfExists: true)] + input[1] = file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/mus_musculus/gene_set_analysis/mh.all.v2022.1.Mm.symbols.gmt", checkIfExists: true) + input[2] = file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/study.filtered.tsv", checkIfExists: true) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.all_enrich, + process.out.plot_png, + process.out.sub_enrich, + process.out.sub_plot, + process.out.filtered_gmt, + process.out.session_info, + process.out.versions, + process.out.plot_html.collect{ meta,html -> file(html).name }, //assert unstable file + process.out.rds.collect{ meta,rds -> file(rds).name } //assert unstable file + ).match() + } + ) + } + } +} diff --git a/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap b/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap new file mode 100644 index 00000000000..ee389b991cd --- /dev/null +++ b/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap @@ -0,0 +1,193 @@ +{ + "test": { + "content": [ + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,1134a02ca061c463bcbff277eefbfb19" + ] + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gprofiler2.gostplot.png:md5,4b83d1bcf7dc9dbf6cef3d545e440c5b" + ] + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + [ + "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,d527b94cdb160070bcaa0bfb0cecf914", + "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,ef418c3f06d50446317928e37ec8ddfb", + "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,e460d4917feb0b64d334a528f59e0731", + "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,865d8f092503552831c51d775a98c6eb", + "Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,413724002abe683f376ea914d4f21ade", + "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,fce81051d7af955ddb2925ba2da9ff57", + "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,e89e1876698ea644671a0720c85f4dbb", + "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,e272217ec7fcf01ea463ab8bcc8335cf", + "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,fdd1efa836d85bb127e933e925290cba" + ] + ] + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + [ + "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.png:md5,d89498267e985adf0ad1266e2deb9f48", + "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.png:md5,e04cdd51b200671613254d021d3af242", + "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.png:md5,33ea0652d78111978677acde0fe7f807", + "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.png:md5,6c040ac4baba73ae5637b00650e6aea1", + "Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.png:md5,fbd232c4eeced95ceda60b43a02dbe1f", + "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.png:md5,956880d3bf4852a06b0ffaaaba565732", + "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.png:md5,0e8f9217d275668986771dc7fede3170", + "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.png:md5,0697164bc87e95e6508db966df94e01e", + "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.png:md5,09976762c7541ff9e5009e8763986845" + ] + ] + ], + [ + + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "R_sessionInfo.log:md5,47643dc530c1a01102cc9db58c1f6b62" + ] + ], + [ + "versions.yml:md5,7ff4ab78463faf97bba7e698ed9a9069" + ], + [ + "Condition_genotype_WT_KO.gprofiler2.gostplot.html" + ], + [ + "Condition_genotype_WT_KO.gprofiler2.gost_results.rds" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2024-12-27T19:16:24.14894842" + }, + "stub": { + "content": [ + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gprofiler2.gostplot.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gprofiler2.*.sub_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gprofiler2.*.sub_enriched_pathways.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.ENSG_filtered.gmt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "versions.yml:md5,7ff4ab78463faf97bba7e698ed9a9069" + ], + [ + "Condition_genotype_WT_KO.gprofiler2.gostplot.html" + ], + [ + "Condition_genotype_WT_KO.gprofiler2.gost_results.rds" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2024-12-27T19:16:37.689819563" + } +} \ No newline at end of file diff --git a/modules/nf-core/gprofiler2/gost/tests/nextflow.config b/modules/nf-core/gprofiler2/gost/tests/nextflow.config new file mode 100644 index 00000000000..1a77344d7ff --- /dev/null +++ b/modules/nf-core/gprofiler2/gost/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.args = params.module_args +} \ No newline at end of file