diff --git a/modules/nf-core/gsea/gsea/main.nf b/modules/nf-core/gsea/gsea/main.nf index 846ded4f44ba..3054f81bcb36 100644 --- a/modules/nf-core/gsea/gsea/main.nf +++ b/modules/nf-core/gsea/gsea/main.nf @@ -43,28 +43,34 @@ process GSEA_GSEA { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def rpt_label = prefix.replaceAll('\\.$', '') // Remove any trailing dots from prefix when passed as report label, so GSEA doesn't produce double-dotted top-level outputs - def chip_command = chip ? "-chip $chip -collapse true" : '' + def rpt_label = prefix.replaceAll('\\.$', '') + def chip_command = chip ? "-chip \"$chip\" -collapse true" : '' + // gsea-cli takes a comma-delimited -gmx value to pool multiple gene set files into one run. + def gmx = gene_sets instanceof List ? gene_sets.join(',') : gene_sets """ # Run GSEA gsea-cli GSEA \\ - -res $gct \\ - -cls ${cls}#${target}_versus_${reference} \\ - -gmx $gene_sets \\ + -res "$gct" \\ + -cls "${cls}#${target}_versus_${reference}" \\ + -gmx "$gmx" \\ $chip_command \\ -out . \\ - --rpt_label $rpt_label \\ + --rpt_label "$rpt_label" \\ $args # Un-timestamp the outputs for path consistency - mv ${rpt_label}.Gsea.*/* . + # Only rmdir actual directories: the .rpt file's name also matches "${rpt_label}.Gsea.*". + mv "$rpt_label".Gsea.*/* . + for gsea_dir in "$rpt_label".Gsea.*/; do + [ -d "\$gsea_dir" ] && rmdir "\$gsea_dir" + done timestamp=\$(cat *.rpt | grep producer_timestamp | awk '{print \$2}') for pattern in _\${timestamp} .\${timestamp}; do find . -name "*\${pattern}*" | sed "s|^\\./||" | while read -r f; do - mv \$f \${f//\$pattern/} + mv "\$f" "\${f//\$pattern/}" done done sed -i.bak "s/[_\\.]\$timestamp//g" *.rpt *.html && rm *.bak diff --git a/modules/nf-core/gsea/gsea/tests/main.nf.test b/modules/nf-core/gsea/gsea/tests/main.nf.test index 9718c6e3d267..479bfbb840c1 100644 --- a/modules/nf-core/gsea/gsea/tests/main.nf.test +++ b/modules/nf-core/gsea/gsea/tests/main.nf.test @@ -59,6 +59,55 @@ nextflow_process { } } + test("test_multiple_gmt") { + + config "./nextflow.config" + + when { + 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/modules/data/genomics/mus_musculus/gene_set_analysis/Condition_treatment_Control_Treated.gct", checkIfExists:true), file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/mus_musculus/gene_set_analysis/Condition_genotype_WT_KO.cls", checkIfExists:true), [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), file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/mus_musculus/gene_set_analysis/m5.mpt.v2022.1.Mm.symbols.gmt", checkIfExists:true)]] + input[1] = ['WT', 'KO'] + input[2] = [ + ['id': 'test'], + file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/mus_musculus/gene_set_analysis/Mus_musculus.anno.feature_metadata.chip", checkIfExists:true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.rpt.collect{ meta,rpt -> file(rpt).name }, //assert unstable file + process.out.index_html.collect{ meta,index_html -> file(index_html).name }, //assert unstable file + process.out.heat_map_corr_plot, + process.out.report_tsvs_ref, + process.out.report_htmls_ref.collect{ meta,report_htmls_ref -> file(report_htmls_ref).name }, //assert unstable file + process.out.report_tsvs_target, + process.out.report_htmls_target.collect{ meta,report_htmls_target -> file(report_htmls_target).name }, //assert unstable file + process.out.ranked_gene_list, + process.out.gene_set_sizes, + process.out.histogram.collect{ meta,histogram -> file(histogram).name }, //assert unstable file + process.out.heatmap.collect{ meta,heatmap -> file(heatmap).name }, //assert unstable file + process.out.pvalues_vs_nes_plot.collect{ meta,pvalues_vs_nes_plot -> file(pvalues_vs_nes_plot).name }, //assert unstable file + process.out.ranked_list_corr.collect{ meta,ranked_list_corr -> file(ranked_list_corr).name }, //assert unstable file + process.out.butterfly_plot.collect{ meta,butterfly_plot -> file(butterfly_plot).name }, //assert unstable file + process.out.gene_set_tsv, + process.out.gene_set_html[0][1].collect{ file(it).name }, //assert unstable file + process.out.gene_set_heatmap[0][1].collect{ file(it).name }, // unstable file and unstable name + process.out.snapshot[0][1].collect{ file(it).name }, //assert unstable file + process.out.gene_set_enplot[0][1].collect{ file(it).name }, // unstable file and unstable name + process.out.gene_set_dist[0][1].collect{ file(it).name }, //assert unstable file + process.out.archive, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() + } + ) + } + } + test("stub") { options "-stub" diff --git a/modules/nf-core/gsea/gsea/tests/main.nf.test.snap b/modules/nf-core/gsea/gsea/tests/main.nf.test.snap index 522b0c078681..534e2762f92b 100644 --- a/modules/nf-core/gsea/gsea/tests/main.nf.test.snap +++ b/modules/nf-core/gsea/gsea/tests/main.nf.test.snap @@ -318,6 +318,340 @@ "nextflow": "25.10.4" } }, + "test_multiple_gmt": { + "content": [ + [ + "Condition_genotype_WT_KO.Gsea.rpt" + ], + [ + "Condition_genotype_WT_KOindex.html" + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KOheat_map_corr_plot.html:md5,129c561984542746bc50c3f6db9c7c5e" + ] + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KOgsea_report_for_WT.tsv:md5,0aadcf1751fc08ba9f3b253ea3c5d3a6" + ] + ], + [ + "Condition_genotype_WT_KOgsea_report_for_WT.html" + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KOgsea_report_for_KO.tsv:md5,21297fb2b50155ed348d83f10ab1ae8b" + ] + ], + [ + "Condition_genotype_WT_KOgsea_report_for_KO.html" + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KOranked_gene_list_KO_versus_WT.tsv:md5,3ae0171ae04398f350cd3e0f183b9d67" + ] + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KOgene_set_sizes.tsv:md5,42fe75837b300bc9c0be6eed72135a1b" + ] + ], + [ + "Condition_genotype_WT_KOglobal_es_histogram.png" + ], + [ + "Condition_genotype_WT_KOheat_map_1.png" + ], + [ + "Condition_genotype_WT_KOpvalues_vs_nes_plot.png" + ], + [ + "Condition_genotype_WT_KOranked_list_corr_2.png" + ], + [ + "Condition_genotype_WT_KObutterfly_plot.png" + ], + [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + [ + "gene_sets_Condition_genotype_WT_KOHALLMARK_ADIPOGENESIS.tsv:md5,0e7035e5cbaba4a35d87538da823e05c", + "gene_sets_Condition_genotype_WT_KOHALLMARK_ANGIOGENESIS.tsv:md5,3b4a7f1b28282bf886c9c06d73f61e45", + "gene_sets_Condition_genotype_WT_KOHALLMARK_APICAL_JUNCTION.tsv:md5,e9d02a848a5aca73a22a6aef7473defd", + "gene_sets_Condition_genotype_WT_KOHALLMARK_APICAL_SURFACE.tsv:md5,84eed15b2aad41077b2a4c5367c05782", + "gene_sets_Condition_genotype_WT_KOHALLMARK_BILE_ACID_METABOLISM.tsv:md5,967e4be880742f32720419fe879b7cc7", + "gene_sets_Condition_genotype_WT_KOHALLMARK_COAGULATION.tsv:md5,6c5bece0e26c1e1b32d9d47b10651baf", + "gene_sets_Condition_genotype_WT_KOHALLMARK_COMPLEMENT.tsv:md5,0d3dfe9073ddbbfa3a6f0c7bcb4c8601", + "gene_sets_Condition_genotype_WT_KOHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION.tsv:md5,122c6786499f76f5ec0c6ce604b52aa0", + "gene_sets_Condition_genotype_WT_KOHALLMARK_ESTROGEN_RESPONSE_EARLY.tsv:md5,7fea0527089b002ccf840223a60ecbf4", + "gene_sets_Condition_genotype_WT_KOHALLMARK_ESTROGEN_RESPONSE_LATE.tsv:md5,a838545de228235bc4f8830b5777e893", + "gene_sets_Condition_genotype_WT_KOHALLMARK_FATTY_ACID_METABOLISM.tsv:md5,926ddf4b74ad3a6d76bc99e82ae6aaf3", + "gene_sets_Condition_genotype_WT_KOHALLMARK_GLYCOLYSIS.tsv:md5,4dcdce8b8db83dd971800f2ff18ccbeb", + "gene_sets_Condition_genotype_WT_KOHALLMARK_HEDGEHOG_SIGNALING.tsv:md5,2d508b31d0ec00228db110a0e9e2f059", + "gene_sets_Condition_genotype_WT_KOHALLMARK_HEME_METABOLISM.tsv:md5,bb723be28feecbbc68909fdb17f8e2f4", + "gene_sets_Condition_genotype_WT_KOHALLMARK_KRAS_SIGNALING_UP.tsv:md5,1b4411d95e2bf08db2bae06996d6729c", + "gene_sets_Condition_genotype_WT_KOHALLMARK_MYOGENESIS.tsv:md5,564c3e924517993e6eac6819a5f53d92", + "gene_sets_Condition_genotype_WT_KOHALLMARK_NOTCH_SIGNALING.tsv:md5,e91e740dac62555b603bf44c427e671e", + "gene_sets_Condition_genotype_WT_KOHALLMARK_OXIDATIVE_PHOSPHORYLATION.tsv:md5,75095d76fc23eccb98d67e045839d4a9", + "gene_sets_Condition_genotype_WT_KOHALLMARK_P53_PATHWAY.tsv:md5,ce4a9fc08c539fc4d930f81e08a2db55", + "gene_sets_Condition_genotype_WT_KOHALLMARK_PEROXISOME.tsv:md5,f0e60a2f8bc511be09ff8f04886eca61", + "gene_sets_Condition_genotype_WT_KOHALLMARK_PROTEIN_SECRETION.tsv:md5,f16a1fcc6e9b4fd976b3c9fefd0f8dc9", + "gene_sets_Condition_genotype_WT_KOHALLMARK_REACTIVE_OXIGEN_SPECIES_PATHWAY.tsv:md5,66bcbea77b774b7d0542abeb460bfef8", + "gene_sets_Condition_genotype_WT_KOHALLMARK_TGF_BETA_SIGNALING.tsv:md5,5970edfc5faad9bb73408d75a2f40350", + "gene_sets_Condition_genotype_WT_KOHALLMARK_UV_RESPONSE_DN.tsv:md5,bb751fac5d95a22e6872ef347038cd4e", + "gene_sets_Condition_genotype_WT_KOHALLMARK_UV_RESPONSE_UP.tsv:md5,8cfe52d138bc42ec8fd7d2c6fbf6761f", + "gene_sets_Condition_genotype_WT_KOHALLMARK_XENOBIOTIC_METABOLISM.tsv:md5,ca28e2bd7b3584d1354e97b09a37f8af", + "gene_sets_Condition_genotype_WT_KOMP_DECREASED_INCIDENCE_OF_TUMORS_BY_CHEMICAL_INDUCTION.tsv:md5,7b29d2bc9cfcc1ff4bcdabd8e46a970b", + "gene_sets_Condition_genotype_WT_KOMP_DECREASED_METASTATIC_POTENTIAL.tsv:md5,c70ceae8d96717f33983442970478710", + "gene_sets_Condition_genotype_WT_KOMP_DECREASED_TUMOR_GROWTH_SIZE.tsv:md5,da6905b554d983629ef19c275fe8724a", + "gene_sets_Condition_genotype_WT_KOMP_DECREASED_TUMOR_NECROSIS_FACTOR_SECRETION.tsv:md5,f318a881241f725ad1de5febd89cd0d2", + "gene_sets_Condition_genotype_WT_KOMP_EMBRYO_TUMOR.tsv:md5,24f94c2c4456aa1f5b773eae810bffb5", + "gene_sets_Condition_genotype_WT_KOMP_INCREASED_ADENOMA_INCIDENCE.tsv:md5,88e9f1759362869157702034e0273169", + "gene_sets_Condition_genotype_WT_KOMP_INCREASED_CARCINOMA_INCIDENCE.tsv:md5,693c20644fd2d9a20f3aa5cf87e3037c", + "gene_sets_Condition_genotype_WT_KOMP_INCREASED_GASTROINTESTINAL_TUMOR_INCIDENCE.tsv:md5,af36f27bcb01c52e9e8bf4b417c26aef", + "gene_sets_Condition_genotype_WT_KOMP_INCREASED_HEMANGIOMA_INCIDENCE.tsv:md5,7741038545f1f9d7bde58f5e338dbdab", + "gene_sets_Condition_genotype_WT_KOMP_INCREASED_HEMANGIOSARCOMA_INCIDENCE.tsv:md5,2f9971d0e21ababd7480812dfda76f6d", + "gene_sets_Condition_genotype_WT_KOMP_INCREASED_HEPATOCELLULAR_CARCINOMA_INCIDENCE.tsv:md5,4ffc87c24f7403067a148d0e92ea7075", + "gene_sets_Condition_genotype_WT_KOMP_INCREASED_LIVER_TUMOR_INCIDENCE.tsv:md5,b5189d8034e7b730f9c35f85aeffe2ae", + "gene_sets_Condition_genotype_WT_KOMP_INCREASED_METASTATIC_POTENTIAL.tsv:md5,0a4a0048b3e87f093ec830aa6707dc8f", + "gene_sets_Condition_genotype_WT_KOMP_INCREASED_TUMOR_NECROSIS_FACTOR_SECRETION.tsv:md5,f6cad28a554d33db2ef536944ee5f884", + "gene_sets_Condition_genotype_WT_KOSymbol_to_probe_set_mapping_details.tsv:md5,a8bed433fe3e8081495c82226ec44917" + ] + ] + ], + [ + "gene_sets_Condition_genotype_WT_KOHALLMARK_ADIPOGENESIS.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_ANGIOGENESIS.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_APICAL_JUNCTION.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_APICAL_SURFACE.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_BILE_ACID_METABOLISM.html", + 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