From 258399c484a25b880fddc9a8dd35b98f371d31f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20Schcolnicov?= <90359308+nschcolnicov@users.noreply.github.com> Date: Mon, 13 Jan 2025 14:30:02 -0300 Subject: [PATCH] Added nftests to gseagsea (#7266) * Added nftests to gseagsea * Update input files * fix nftests * Address PR comments * Add seed setting parameter for stabilizing results * Fix linting * Add default random seed * Update datasets paths --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- modules/nf-core/gsea/gsea/main.nf | 92 ++- modules/nf-core/gsea/gsea/meta.yml | 13 +- modules/nf-core/gsea/gsea/tests/main.nf.test | 78 ++ .../nf-core/gsea/gsea/tests/main.nf.test.snap | 692 ++++++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/gsea/gsea/main.nf | 53 -- .../modules/nf-core/gsea/gsea/nextflow.config | 18 - tests/modules/nf-core/gsea/gsea/test.yml | 653 ----------------- 8 files changed, 853 insertions(+), 749 deletions(-) create mode 100644 modules/nf-core/gsea/gsea/tests/main.nf.test create mode 100644 modules/nf-core/gsea/gsea/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/gsea/gsea/main.nf delete mode 100644 tests/modules/nf-core/gsea/gsea/nextflow.config delete mode 100644 tests/modules/nf-core/gsea/gsea/test.yml diff --git a/modules/nf-core/gsea/gsea/main.nf b/modules/nf-core/gsea/gsea/main.nf index 6a060c46582..2cc542dc989 100644 --- a/modules/nf-core/gsea/gsea/main.nf +++ b/modules/nf-core/gsea/gsea/main.nf @@ -4,8 +4,8 @@ process GSEA_GSEA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gsea:4.3.2--hdfd78af_0': - 'biocontainers/gsea:4.3.2--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0f/0f4fe28961396eeeaa98484cb4f2db5c79abfdf117700df132312fe5c41bff81/data': + 'community.wave.seqera.io/library/gsea:4.3.2--a7421d7504fd7c81' }" input: tuple val(meta), path(gct), path(cls), path(gene_sets) @@ -26,29 +26,27 @@ process GSEA_GSEA { tuple val(meta), path("*heat_map_1.png") , emit: heatmap tuple val(meta), path("*pvalues_vs_nes_plot.png") , emit: pvalues_vs_nes_plot tuple val(meta), path("*ranked_list_corr_2.png") , emit: ranked_list_corr - tuple val(meta), path("*butterfly_plot.png") , emit: butterfly_plot, optional: true - tuple val(meta), path("*[!gene_set_size|gsea_report|ranked_gene_list]*.tsv"), emit: gene_set_tsv, optional: true - tuple val(meta), path("*[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html"), emit: gene_set_html, optional: true - tuple val(meta), path("*[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png"), emit: gene_set_heatmap, optional: true - tuple val(meta), path("*_snapshot*.html") , emit: snapshot, optional: true - tuple val(meta), path("*enplot*.png") , emit: gene_set_enplot, optional: true - tuple val(meta), path("*gset_rnd_es_dist*.png") , emit: gene_set_dist, optional: true - tuple val(meta), path("*.zip") , emit: archive, optional: true + tuple val(meta), path("*butterfly_plot.png") , emit: butterfly_plot , optional: true + tuple val(meta), path("gene_sets_*.tsv") , emit: gene_set_tsv , optional: true + tuple val(meta), path("gene_sets_*.html") , emit: gene_set_html , optional: true + tuple val(meta), path("gene_sets_*.png") , emit: gene_set_heatmap, optional: true + tuple val(meta), path("*_snapshot*.html") , emit: snapshot , optional: true + tuple val(meta), path("*enplot*.png") , emit: gene_set_enplot , optional: true + tuple val(meta), path("*gset_rnd_es_dist*.png") , emit: gene_set_dist , optional: true + tuple val(meta), path("*.zip") , emit: archive , optional: true path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def VERSION = '4.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - - // Remove any trailing dots from prefix when passed as report label, so - // GSEA doesn't produce double-dotted top-level outputs - def rpt_label = prefix.replaceAll('\\.$', '') - + 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 $chip -collapse true" : '' + def VERSION = '4.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + if (!(args ==~ /.*-rnd_seed.*/)) {args += " -rnd_seed 10"} + """ # Run GSEA @@ -78,9 +76,71 @@ process GSEA_GSEA { sed -i.bak "s/\$f/${prefix}\${f}/g" *.rpt *.html && rm *.bak done + # Rename files so that they can be properly referenced by the output channels + # Function to rename files based on the given pattern + rename_files() { + local pattern=\$1 + local exclude_patterns=\$2 + local extension=\$3 + + # Find files matching the pattern but not matching the exclusion patterns + find . -type f -name "\$pattern" | while read -r file; do + # Exclude files based on the provided exclusion patterns + if ! echo "\$file" | grep -qE "\$exclude_patterns"; then + # Rename the file by adding the prefix "gene_sets_" + mv "\$file" "\$(dirname "\$file")/gene_sets_\$(basename "\$file")" + fi + done + } + + # Pattern and exclusion for .tsv files + tsv_pattern="*.tsv" + tsv_exclude="gene_set_size|gsea_report|ranked_gene_list" + + # Pattern and exclusion for .html files + html_pattern="*.html" + html_exclude="gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot" + + # Pattern and exclusion for .png files + png_pattern="*.png" + png_exclude="butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr" + + # Rename .tsv files + rename_files "\$tsv_pattern" "\$tsv_exclude" ".tsv" + + # Rename .html files + rename_files "\$html_pattern" "\$html_exclude" ".html" + + # Rename .png files + rename_files "\$png_pattern" "\$png_exclude" ".png" + + cat <<-END_VERSIONS > versions.yml "${task.process}": gsea: $VERSION END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '4.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + touch ${prefix}.rpt + touch ${prefix}.index.html + touch ${prefix}.heat_map_corr_plot.html + touch ${prefix}.gsea_report_for_${reference}.tsv + touch ${prefix}.gsea_report_for_${reference}.html + touch ${prefix}.gsea_report_for_${target}.tsv + touch ${prefix}.gsea_report_for_${target}.html + touch ${prefix}.ranked_gene_list*.tsv + touch ${prefix}.gene_set_sizes.tsv + touch ${prefix}.global_es_histogram.png + touch ${prefix}.heat_map_1.png + touch ${prefix}.pvalues_vs_nes_plot.png + touch ${prefix}.ranked_list_corr_2.png + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gsea: $VERSION + """ } diff --git a/modules/nf-core/gsea/gsea/meta.yml b/modules/nf-core/gsea/gsea/meta.yml index f3ce403fd04..937d3a6ac4b 100644 --- a/modules/nf-core/gsea/gsea/meta.yml +++ b/modules/nf-core/gsea/gsea/meta.yml @@ -182,31 +182,31 @@ output: type: map description: | Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] - - "*[!gene_set_size|gsea_report|ranked_gene_list]*.tsv": + - "gene_sets_*.tsv": type: list description: Where -make_sets is not set to false, TSV files, one file for each gene set, with detail on enrichment for each gene - pattern: "[!gene_set_size|gsea_report|ranked_gene_list]*.tsv" + pattern: "gene_sets_*.tsv" - gene_set_html: - meta: type: map description: | Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] - - "*[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html": + - "gene_sets_*.html": type: list description: Where -make_sets is not set to false, HTML files, one file for each gene set, with detail on enrichment for each gene - pattern: "[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html" + pattern: "gene_sets_*.html" - gene_set_heatmap: - meta: type: map description: | Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] - - "*[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png": + - "gene_sets_*.png": type: list description: Where -make_sets is not set to false, PNG-format heatmaps, one file for each gene set, showing expression for each gene - pattern: "[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png" + pattern: "gene_sets_*.png" - snapshot: - meta: type: map @@ -255,3 +255,4 @@ authors: - "@pinin4fjords" maintainers: - "@pinin4fjords" + - "@nschcolnicov" diff --git a/modules/nf-core/gsea/gsea/tests/main.nf.test b/modules/nf-core/gsea/gsea/tests/main.nf.test new file mode 100644 index 00000000000..869cf0ca0ef --- /dev/null +++ b/modules/nf-core/gsea/gsea/tests/main.nf.test @@ -0,0 +1,78 @@ +nextflow_process { + + name "Test Process GSEA_GSEA" + script "../main.nf" + process "GSEA_GSEA" + + tag "modules" + tag "modules_nfcore" + tag "gsea_gsea" + tag "gsea" + tag "gsea/gsea" + + test("test") { + + 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)] + input[1] = ['WT', 'KO'] + input[2] = 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.versions + ).match() + } + ) + } + } + + test("stub") { + + options "-stub" + + 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)] + input[1] = ['WT', 'KO'] + input[2] = 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).match() }, + ) + } + } +} diff --git a/modules/nf-core/gsea/gsea/tests/main.nf.test.snap b/modules/nf-core/gsea/gsea/tests/main.nf.test.snap new file mode 100644 index 00000000000..5ed2fe53c03 --- /dev/null +++ b/modules/nf-core/gsea/gsea/tests/main.nf.test.snap @@ -0,0 +1,692 @@ +{ + "test": { + "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:md5,674b21a1646cc554d6686ddd67c55dab" + ] + ], + [ + "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,a4e7de6cf0400befc6e52e379c89c178" + ] + ], + [ + "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:md5,61ca77f6b13620a78170c0b9366b8425" + ] + ], + [ + "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_ANDROGEN_RESPONSE.tsv:md5,46cee22eddeac12e1d8643e539c6c397", + "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_APOPTOSIS.tsv:md5,302c2afbf1b77c6eccd7983fb657007c", + "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_DNA_REPAIR.tsv:md5,975b4b3905685e73500ec49cd54a2c03", + "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_HYPOXIA.tsv:md5,e3a7d53519ee12377377659743d9cf4c", + "gene_sets_Condition_genotype_WT_KOHALLMARK_IL2_STAT5_SIGNALING.tsv:md5,4bcc7835887602c732c85ef2db4f5584", + "gene_sets_Condition_genotype_WT_KOHALLMARK_IL6_JAK_STAT3_SIGNALING.tsv:md5,18e50d2154c81700b2c44ee848ced133", + "gene_sets_Condition_genotype_WT_KOHALLMARK_INTERFERON_ALPHA_RESPONSE.tsv:md5,fb6fcf993118271ee3340e9a12de0ed7", + "gene_sets_Condition_genotype_WT_KOHALLMARK_KRAS_SIGNALING_DN.tsv:md5,d0649d9c33c0f81bf4e8e2dcdb6a036d", + "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_PANCREAS_BETA_CELLS.tsv:md5,9df68cbfc6e4666d18ff6d214c5f1544", + "gene_sets_Condition_genotype_WT_KOHALLMARK_PEROXISOME.tsv:md5,f0e60a2f8bc511be09ff8f04886eca61", + "gene_sets_Condition_genotype_WT_KOHALLMARK_PI3K_AKT_MTOR_SIGNALING.tsv:md5,f76d919c3e1342304bb69e50a58c81d9", + "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_WNT_BETA_CATENIN_SIGNALING.tsv:md5,b45d874ea3fdd7cd4f8bd09843eaa941", + "gene_sets_Condition_genotype_WT_KOHALLMARK_XENOBIOTIC_METABOLISM.tsv:md5,ca28e2bd7b3584d1354e97b09a37f8af", + "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_ANDROGEN_RESPONSE.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_APOPTOSIS.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_BILE_ACID_METABOLISM.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_COAGULATION.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_COMPLEMENT.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_DNA_REPAIR.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_ESTROGEN_RESPONSE_EARLY.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_ESTROGEN_RESPONSE_LATE.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_FATTY_ACID_METABOLISM.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_GLYCOLYSIS.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_HEDGEHOG_SIGNALING.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_HEME_METABOLISM.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_HYPOXIA.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_IL2_STAT5_SIGNALING.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_IL6_JAK_STAT3_SIGNALING.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_INTERFERON_ALPHA_RESPONSE.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_KRAS_SIGNALING_DN.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_KRAS_SIGNALING_UP.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_MYOGENESIS.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_NOTCH_SIGNALING.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_OXIDATIVE_PHOSPHORYLATION.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_P53_PATHWAY.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_PANCREAS_BETA_CELLS.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_PEROXISOME.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_PI3K_AKT_MTOR_SIGNALING.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_PROTEIN_SECRETION.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_REACTIVE_OXIGEN_SPECIES_PATHWAY.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_TGF_BETA_SIGNALING.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_UV_RESPONSE_DN.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_UV_RESPONSE_UP.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_WNT_BETA_CATENIN_SIGNALING.html", + "gene_sets_Condition_genotype_WT_KOHALLMARK_XENOBIOTIC_METABOLISM.html" + ], + [ + "gene_sets_Condition_genotype_WT_KOHALLMARK_ADIPOGENESIS_13.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_ANDROGEN_RESPONSE_100.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_ANGIOGENESIS_94.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_APICAL_JUNCTION_55.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_APICAL_SURFACE_82.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_APOPTOSIS_40.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_BILE_ACID_METABOLISM_31.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_COAGULATION_34.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_COMPLEMENT_91.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_DNA_REPAIR_43.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION_67.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_ESTROGEN_RESPONSE_EARLY_58.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_ESTROGEN_RESPONSE_LATE_70.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_FATTY_ACID_METABOLISM_16.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_GLYCOLYSIS_97.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_HEDGEHOG_SIGNALING_61.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_HEME_METABOLISM_28.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_HYPOXIA_103.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_IL2_STAT5_SIGNALING_106.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_IL6_JAK_STAT3_SIGNALING_46.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_INTERFERON_ALPHA_RESPONSE_52.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_KRAS_SIGNALING_DN_109.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_KRAS_SIGNALING_UP_85.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_MYOGENESIS_64.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_NOTCH_SIGNALING_73.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_OXIDATIVE_PHOSPHORYLATION_4.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_P53_PATHWAY_22.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_PANCREAS_BETA_CELLS_37.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_PEROXISOME_7.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_PI3K_AKT_MTOR_SIGNALING_49.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_PROTEIN_SECRETION_10.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_REACTIVE_OXIGEN_SPECIES_PATHWAY_25.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_TGF_BETA_SIGNALING_79.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_UV_RESPONSE_DN_76.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_UV_RESPONSE_UP_88.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_WNT_BETA_CATENIN_SIGNALING_112.png", + "gene_sets_Condition_genotype_WT_KOHALLMARK_XENOBIOTIC_METABOLISM_19.png" + ], + [ + "Condition_genotype_WT_KOneg_snapshot.html", + "Condition_genotype_WT_KOpos_snapshot.html" + ], + [ + "Condition_genotype_WT_KOenplot_HALLMARK_ADIPOGENESIS_12.png", + "Condition_genotype_WT_KOenplot_HALLMARK_ANDROGEN_RESPONSE_99.png", + "Condition_genotype_WT_KOenplot_HALLMARK_ANGIOGENESIS_93.png", + "Condition_genotype_WT_KOenplot_HALLMARK_APICAL_JUNCTION_54.png", + "Condition_genotype_WT_KOenplot_HALLMARK_APICAL_SURFACE_81.png", + "Condition_genotype_WT_KOenplot_HALLMARK_APOPTOSIS_39.png", + "Condition_genotype_WT_KOenplot_HALLMARK_BILE_ACID_METABOLISM_30.png", + "Condition_genotype_WT_KOenplot_HALLMARK_COAGULATION_33.png", + "Condition_genotype_WT_KOenplot_HALLMARK_COMPLEMENT_90.png", + "Condition_genotype_WT_KOenplot_HALLMARK_DNA_REPAIR_42.png", + "Condition_genotype_WT_KOenplot_HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION_66.png", + "Condition_genotype_WT_KOenplot_HALLMARK_ESTROGEN_RESPONSE_EARLY_57.png", + "Condition_genotype_WT_KOenplot_HALLMARK_ESTROGEN_RESPONSE_LATE_69.png", + "Condition_genotype_WT_KOenplot_HALLMARK_FATTY_ACID_METABOLISM_15.png", + "Condition_genotype_WT_KOenplot_HALLMARK_GLYCOLYSIS_96.png", + "Condition_genotype_WT_KOenplot_HALLMARK_HEDGEHOG_SIGNALING_60.png", + "Condition_genotype_WT_KOenplot_HALLMARK_HEME_METABOLISM_27.png", + "Condition_genotype_WT_KOenplot_HALLMARK_HYPOXIA_102.png", + "Condition_genotype_WT_KOenplot_HALLMARK_IL2_STAT5_SIGNALING_105.png", + "Condition_genotype_WT_KOenplot_HALLMARK_IL6_JAK_STAT3_SIGNALING_45.png", + "Condition_genotype_WT_KOenplot_HALLMARK_INTERFERON_ALPHA_RESPONSE_51.png", + "Condition_genotype_WT_KOenplot_HALLMARK_KRAS_SIGNALING_DN_108.png", + "Condition_genotype_WT_KOenplot_HALLMARK_KRAS_SIGNALING_UP_84.png", + "Condition_genotype_WT_KOenplot_HALLMARK_MYOGENESIS_63.png", + "Condition_genotype_WT_KOenplot_HALLMARK_NOTCH_SIGNALING_72.png", + "Condition_genotype_WT_KOenplot_HALLMARK_OXIDATIVE_PHOSPHORYLATION_3.png", + "Condition_genotype_WT_KOenplot_HALLMARK_P53_PATHWAY_21.png", + "Condition_genotype_WT_KOenplot_HALLMARK_PANCREAS_BETA_CELLS_36.png", + "Condition_genotype_WT_KOenplot_HALLMARK_PEROXISOME_6.png", + "Condition_genotype_WT_KOenplot_HALLMARK_PI3K_AKT_MTOR_SIGNALING_48.png", + "Condition_genotype_WT_KOenplot_HALLMARK_PROTEIN_SECRETION_9.png", + "Condition_genotype_WT_KOenplot_HALLMARK_REACTIVE_OXIGEN_SPECIES_PATHWAY_24.png", + "Condition_genotype_WT_KOenplot_HALLMARK_TGF_BETA_SIGNALING_78.png", + "Condition_genotype_WT_KOenplot_HALLMARK_UV_RESPONSE_DN_75.png", + "Condition_genotype_WT_KOenplot_HALLMARK_UV_RESPONSE_UP_87.png", + "Condition_genotype_WT_KOenplot_HALLMARK_WNT_BETA_CATENIN_SIGNALING_111.png", + "Condition_genotype_WT_KOenplot_HALLMARK_XENOBIOTIC_METABOLISM_18.png" + ], + [ + "Condition_genotype_WT_KOgset_rnd_es_dist_101.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_104.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_107.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_11.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_110.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_113.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_14.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_17.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_20.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_23.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_26.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_29.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_32.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_35.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_38.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_41.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_44.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_47.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_5.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_50.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_53.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_56.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_59.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_62.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_65.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_68.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_71.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_74.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_77.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_8.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_80.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_83.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_86.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_89.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_92.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_95.png", + "Condition_genotype_WT_KOgset_rnd_es_dist_98.png" + ], + [ + + ], + [ + "versions.yml:md5,957596d9ab6aad1125546a4279696a38" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-01-09T12:59:01.403655519" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.rpt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.index.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.heat_map_1.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "11": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.pvalues_vs_nes_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "12": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.ranked_list_corr_2.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "13": [ + + ], + "14": [ + + ], + "15": [ + + ], + "16": [ + + ], + "17": [ + + ], + "18": [ + + ], + "19": [ + + ], + "2": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.heat_map_corr_plot.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "20": [ + + ], + "21": [ + "versions.yml:md5,957596d9ab6aad1125546a4279696a38" + ], + "3": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gsea_report_for_WT.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gsea_report_for_WT.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gsea_report_for_KO.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gsea_report_for_KO.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "7": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.ranked_gene_list*.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gene_set_sizes.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "9": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.global_es_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "archive": [ + + ], + "butterfly_plot": [ + + ], + "gene_set_dist": [ + + ], + "gene_set_enplot": [ + + ], + "gene_set_heatmap": [ + + ], + "gene_set_html": [ + + ], + "gene_set_sizes": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gene_set_sizes.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gene_set_tsv": [ + + ], + "heat_map_corr_plot": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.heat_map_corr_plot.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "heatmap": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.heat_map_1.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "histogram": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.global_es_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "index_html": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.index.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "pvalues_vs_nes_plot": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.pvalues_vs_nes_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "ranked_gene_list": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.ranked_gene_list*.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "ranked_list_corr": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.ranked_list_corr_2.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "report_htmls_ref": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gsea_report_for_WT.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "report_htmls_target": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gsea_report_for_KO.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "report_tsvs_ref": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gsea_report_for_WT.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "report_tsvs_target": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.gsea_report_for_KO.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "rpt": [ + [ + { + "id": "Condition_genotype_WT_KO", + "variable": "Condition genotype", + "reference": "WT", + "target": "KO", + "blocking": "batch" + }, + "Condition_genotype_WT_KO.rpt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "snapshot": [ + + ], + "versions": [ + "versions.yml:md5,957596d9ab6aad1125546a4279696a38" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-01-08T17:41:24.591802253" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 1dfa854152f..1dfd96fce1e 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -206,9 +206,6 @@ grids/gridsssomaticfilter: gridss/gridssgenerateponbedpe: - modules/nf-core/gridss/gridssgenerateponbedpe/** - tests/modules/nf-core/gridss/gridssgenerateponbedpe/** -gsea/gsea: - - modules/nf-core/gsea/gsea/** - - tests/modules/nf-core/gsea/gsea/** hlala/preparegraph: - modules/nf-core/hlala/preparegraph/** - tests/modules/nf-core/hlala/preparegraph/** diff --git a/tests/modules/nf-core/gsea/gsea/main.nf b/tests/modules/nf-core/gsea/gsea/main.nf deleted file mode 100644 index 8eedfe6f6dc..00000000000 --- a/tests/modules/nf-core/gsea/gsea/main.nf +++ /dev/null @@ -1,53 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GSEA_GSEA } from '../../../../../modules/nf-core/gsea/gsea/main.nf' - -workflow test_gsea_gsea { - - gct_file = file(params.test_data['homo_sapiens']['gene_set_analysis']['gct'], checkIfExists: true) - cls_file = file(params.test_data['homo_sapiens']['gene_set_analysis']['cls'], checkIfExists: true) - gmx_file = file(params.test_data['homo_sapiens']['gene_set_analysis']['gmx'], checkIfExists: true) - - input = [ ['id': 'study' ], gct_file, cls_file, gmx_file ] - contrast = [ 'WT', 'MUT' ] - - GSEA_GSEA ( - input, - contrast, - [] - ) -} - -workflow test_gsea_gsea_nosets { - - gct_file = file(params.test_data['homo_sapiens']['gene_set_analysis']['gct'], checkIfExists: true) - cls_file = file(params.test_data['homo_sapiens']['gene_set_analysis']['cls'], checkIfExists: true) - gmx_file = file(params.test_data['homo_sapiens']['gene_set_analysis']['gmx'], checkIfExists: true) - - input = [ ['id': 'study' ], gct_file, cls_file, gmx_file ] - contrast = [ 'WT', 'MUT' ] - - GSEA_GSEA ( - input, - contrast, - [] - ) -} - -workflow test_gsea_gsea_zip { - - gct_file = file(params.test_data['homo_sapiens']['gene_set_analysis']['gct'], checkIfExists: true) - cls_file = file(params.test_data['homo_sapiens']['gene_set_analysis']['cls'], checkIfExists: true) - gmx_file = file(params.test_data['homo_sapiens']['gene_set_analysis']['gmx'], checkIfExists: true) - - input = [ ['id': 'study' ], gct_file, cls_file, gmx_file ] - contrast = [ 'WT', 'MUT' ] - - GSEA_GSEA ( - input, - contrast, - [] - ) -} diff --git a/tests/modules/nf-core/gsea/gsea/nextflow.config b/tests/modules/nf-core/gsea/gsea/nextflow.config deleted file mode 100644 index 73d35251bd5..00000000000 --- a/tests/modules/nf-core/gsea/gsea/nextflow.config +++ /dev/null @@ -1,18 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: 'test_gsea_gsea:GSEA_GSEA' { - ext.prefix = { "${meta.id}." } - ext.args = { "-rnd_seed 1234" } - } - withName: 'test_gsea_gsea_nosets:GSEA_GSEA' { - ext.prefix = { "${meta.id}." } - ext.args = { "-rnd_seed 1234 -make_sets false" } - } - - withName: 'test_gsea_gsea_zip:GSEA_GSEA' { - ext.prefix = { "${meta.id}." } - ext.args = { "-rnd_seed 1234 -zip_report true" } - } -} diff --git a/tests/modules/nf-core/gsea/gsea/test.yml b/tests/modules/nf-core/gsea/gsea/test.yml deleted file mode 100644 index cb00f218e2c..00000000000 --- a/tests/modules/nf-core/gsea/gsea/test.yml +++ /dev/null @@ -1,653 +0,0 @@ -- name: gsea gsea test_gsea_gsea - command: nextflow run ./tests/modules/nf-core/gsea/gsea -entry test_gsea_gsea -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gsea/gsea/nextflow.config - tags: - - gsea - - gsea/gsea - files: - - path: output/gsea/study.Gsea.rpt - - path: output/gsea/study.CHR10.html - md5sum: 22919353bea41f7d714d8226482da1e4 - - path: output/gsea/study.CHR10.tsv - md5sum: 73a9336964c5bc78a85f4565a0deb936 - - path: output/gsea/study.CHR10Q21.html - md5sum: 785bf0d2fc2a4cb02f09b840faad92cc - - path: output/gsea/study.CHR10Q21.tsv - md5sum: 7026b101ef8904656c694f6d84d6dce1 - - path: output/gsea/study.CHR10Q21_40.png - - path: output/gsea/study.CHR10Q22.html - md5sum: 026645b0de3a33f0dce387be02d0c674 - - path: output/gsea/study.CHR10Q22.tsv - md5sum: 117663090e727b6b9b5b2f0fc18efaf7 - - path: output/gsea/study.CHR10Q22_19.png - - path: output/gsea/study.CHR10Q23.html - md5sum: 648b1a145ee38a8ad738677246ad4239 - - path: output/gsea/study.CHR10Q23.tsv - md5sum: 3bbd95fda5becfedb275bed0252497b3 - - path: output/gsea/study.CHR10Q23_10.png - - path: output/gsea/study.CHR10Q24.html - md5sum: ee20a6beacfd1f9313f522ce3cd22029 - - path: output/gsea/study.CHR10Q24.tsv - md5sum: 30f70efdd016b85dddfe8f2ac82c8818 - - path: output/gsea/study.CHR10Q24_52.png - - path: output/gsea/study.CHR10_28.png - - path: output/gsea/study.CHR11Q23.html - md5sum: 9a2e7f1a6787cc68e9e0a342431b7614 - - path: output/gsea/study.CHR11Q23.tsv - md5sum: 3d434bb07f5bfe75485313ce691d3b6f - - path: output/gsea/study.CHR11Q23_97.png - - path: output/gsea/study.CHR12.html - md5sum: 156331b5bee99f3855d644c57598c704 - - path: output/gsea/study.CHR12.tsv - md5sum: c59642e40feaebe8740dbedc963395d3 - - path: output/gsea/study.CHR12Q13.html - md5sum: 1e769f3364cffbf86b3845f376b2971f - - path: output/gsea/study.CHR12Q13.tsv - md5sum: 738af83f3d0a0d5ce3487abf2dbea9ca - - path: output/gsea/study.CHR12Q13_64.png - - path: output/gsea/study.CHR12_73.png - - path: output/gsea/study.CHR14.html - md5sum: 164768ee86f5546a3700d72e275644a8 - - path: output/gsea/study.CHR14.tsv - md5sum: 2b91e27831b2650fa84aebcd39c95910 - - path: output/gsea/study.CHR14Q32.html - md5sum: ec08060c3f8409ff277bf4a3c0da9cd1 - - path: output/gsea/study.CHR14Q32.tsv - md5sum: a59ffab651e71d6c6c21eb090452002f - - path: output/gsea/study.CHR14Q32_34.png - - path: output/gsea/study.CHR14_55.png - - path: output/gsea/study.CHR15Q24.html - md5sum: 2c937be23905f4abbdd89a9221b87ed9 - - path: output/gsea/study.CHR15Q24.tsv - md5sum: c3df349a38d4e13f21daee85c49cd727 - - path: output/gsea/study.CHR15Q24_115.png - - path: output/gsea/study.CHR16P12.html - md5sum: 2b473e0db606b01d678058fdb344734c - - path: output/gsea/study.CHR16P12.tsv - md5sum: 2d4b96f20c566208fc129ecb5ddc7def - - path: output/gsea/study.CHR16P12_112.png - - path: output/gsea/study.CHR16Q24.html - md5sum: 6ed25f51b439a18c6ef687b5ad4d747f - - path: output/gsea/study.CHR16Q24.tsv - md5sum: 8068bae266be3f040d55830f3d814623 - - path: output/gsea/study.CHR16Q24_82.png - - path: output/gsea/study.CHR17Q21.html - md5sum: e3b0cf7fac28a00739ca7c00d6e8bd47 - - path: output/gsea/study.CHR17Q21.tsv - md5sum: c1fe27de29f21e3585633579067f633e - - path: output/gsea/study.CHR17Q21_91.png - - path: output/gsea/study.CHR18.html - md5sum: dbab621e91e1f8182b2be5f01439d57c - - path: output/gsea/study.CHR18.tsv - md5sum: aa04a24e5de913dc3879d79b489ab156 - - path: output/gsea/study.CHR18P11.html - md5sum: 2547bf6806442d7800e1cf75272f7cea - - path: output/gsea/study.CHR18P11.tsv - md5sum: a878a99c5a0614e51f048c51a8c8844c - - path: output/gsea/study.CHR18P11_37.png - - path: output/gsea/study.CHR18_61.png - - path: output/gsea/study.CHR1P22.html - md5sum: 0a8ab68e52d6604934b11f45cbc4a9d9 - - path: output/gsea/study.CHR1P22.tsv - md5sum: 630d24e29c17c977637545d55557df5a - - path: output/gsea/study.CHR1P22_25.png - - path: output/gsea/study.CHR1Q21.html - md5sum: 8ae41e08e44cfad7adcd46faf0eed4a0 - - path: output/gsea/study.CHR1Q21.tsv - md5sum: 05a625ffbadcfcb46e2ce7aaaba69f55 - - path: output/gsea/study.CHR1Q21_67.png - - path: output/gsea/study.CHR20.html - md5sum: 7ab53b0e86e6d9e77c63c1a2d2039175 - - path: output/gsea/study.CHR20.tsv - md5sum: ddc1bf49facaf8d2ad83753586e5f38a - - path: output/gsea/study.CHR20_121.png - - path: output/gsea/study.CHR21.html - md5sum: a62c8f2fb79497267638e36a395a1a10 - - path: output/gsea/study.CHR21.tsv - md5sum: 3b513bbfa4e990678bdd6a47003f3941 - - path: output/gsea/study.CHR21_16.png - - path: output/gsea/study.CHR22.html - md5sum: 7dc0cc399d036632c1c72767497cc41b - - path: output/gsea/study.CHR22.tsv - md5sum: 31ef37c7f3610ad803286331f690cbe4 - - path: output/gsea/study.CHR22Q12.html - md5sum: 4dacaae6030467e4eb83c7026b30624c - - path: output/gsea/study.CHR22Q12.tsv - md5sum: cf438ec5cd399de1c6b7ff65deae4307 - - path: output/gsea/study.CHR22Q12_94.png - - path: output/gsea/study.CHR22_118.png - - path: output/gsea/study.CHR2P13.html - md5sum: 3deb087e62e43043e345f30f17474abc - - path: output/gsea/study.CHR2P13.tsv - md5sum: 30064c1421b921c2d69f3451143d45ea - - path: output/gsea/study.CHR2P13_88.png - - path: output/gsea/study.CHR2P23.html - md5sum: 00bc73a37818fc5b6d05122c0c773b81 - - path: output/gsea/study.CHR2P23.tsv - md5sum: de3a0040f744308804e0f57a29129794 - - path: output/gsea/study.CHR2P23_70.png - - path: output/gsea/study.CHR2Q35.html - md5sum: 13f50b1d01ad8d3f669250e3c25c618c - - path: output/gsea/study.CHR2Q35.tsv - md5sum: aad72e817f5373cd12ea11b1acc4577d - - path: output/gsea/study.CHR2Q35_109.png - - path: output/gsea/study.CHR3P14.html - md5sum: 23fcd9ca3527d01c00cb29b2b5f1e3f1 - - path: output/gsea/study.CHR3P14.tsv - md5sum: 9376e3a9b3043d0725780f69a17dd468 - - path: output/gsea/study.CHR3P14_103.png - - path: output/gsea/study.CHR3P24.html - md5sum: 04ac2985e35c3d6db3133b6da097559d - - path: output/gsea/study.CHR3P24.tsv - md5sum: e326b4c1221b19b1ab17feede9e637c6 - - path: output/gsea/study.CHR3P24_100.png - - path: output/gsea/study.CHR3Q13.html - md5sum: d464dce4ebe5b695604ad15d56731a1e - - path: output/gsea/study.CHR3Q13.tsv - md5sum: 8bf0fb21b6ef7e9c67a83dabb8f91fe8 - - path: output/gsea/study.CHR3Q13_76.png - - path: output/gsea/study.CHR3Q27.html - md5sum: 0bf3f1bde949cded670357dda848bacf - - path: output/gsea/study.CHR3Q27.tsv - md5sum: 5d0eb188521981403c0a225e14f25cbe - - path: output/gsea/study.CHR3Q27_85.png - - path: output/gsea/study.CHR5.html - md5sum: a14172ec4cce737c20294222d518bb1a - - path: output/gsea/study.CHR5.tsv - md5sum: 78a09348dada4ded4e2c921bad2ba17c - - path: output/gsea/study.CHR5Q23.html - md5sum: 2a9f47155465c1486795d7513a895e6e - - path: output/gsea/study.CHR5Q23.tsv - md5sum: cf359fb8a320710d2294754abe5dd61b - - path: output/gsea/study.CHR5Q23_43.png - - path: output/gsea/study.CHR5Q31.html - md5sum: d5d3d54cf4c9a76e125ca552f6d7a2e6 - - path: output/gsea/study.CHR5Q31.tsv - md5sum: 144563bca2cdebb9b8cd7e677f41d936 - - path: output/gsea/study.CHR5Q31_7.png - - path: output/gsea/study.CHR5Q32.html - md5sum: 446fae10b9187163f2936715d1d7b2cf - - path: output/gsea/study.CHR5Q32.tsv - md5sum: 212ed9ad35446bc75d56251c23051be5 - - path: output/gsea/study.CHR5Q32_106.png - - path: output/gsea/study.CHR5_31.png - - path: output/gsea/study.CHR6.html - md5sum: b187b1fe265811e702710f4d240c0c42 - - path: output/gsea/study.CHR6.tsv - md5sum: ad9701adf3e508cbeed5b2f6e5534d0c - - path: output/gsea/study.CHR6Q14.html - md5sum: 3315f95af4f834c73e2ee099b7615fc4 - - path: output/gsea/study.CHR6Q14.tsv - md5sum: 468463d60a086cbc7e88d08ede904685 - - path: output/gsea/study.CHR6Q14_22.png - - path: output/gsea/study.CHR6_58.png - - path: output/gsea/study.CHR7P14.html - md5sum: 177d25c4b8615dff187df2ae4a4bd9eb - - path: output/gsea/study.CHR7P14.tsv - md5sum: db965bfea6402110577c9d4fc3dc91e4 - - path: output/gsea/study.CHR7P14_79.png - - path: output/gsea/study.CHR8Q21.html - md5sum: fd6cd66e5c3e128f0ff56da063ad4244 - - path: output/gsea/study.CHR8Q21.tsv - md5sum: 0291f59a2ecb181bbd356fab4d594207 - - path: output/gsea/study.CHR8Q21_4.png - - path: output/gsea/study.CHR9.html - md5sum: b338456b097db4a7cf7fe2eeb29b0052 - - path: output/gsea/study.CHR9.tsv - md5sum: 4e3dad7570a62a11af1d9fbb7481c69a - - path: output/gsea/study.CHR9Q34.html - md5sum: 75ba9004056409c549cb87e9fd8bbdcd - - path: output/gsea/study.CHR9Q34.tsv - md5sum: 1f6e7e63127d79bafe049426c8c1e329 - - path: output/gsea/study.CHR9Q34_46.png - - path: output/gsea/study.CHR9_49.png - - path: output/gsea/study.CHRXQ26.html - md5sum: 78636c92206c543c28f3f41512afb75f - - path: output/gsea/study.CHRXQ26.tsv - md5sum: 5ea132360f57ab160d0f0b5fcc71e52e - - path: output/gsea/study.CHRXQ26_13.png - - path: output/gsea/study.butterfly_plot.png - - path: output/gsea/study.enplot_CHR10Q21_39.png - - path: output/gsea/study.enplot_CHR10Q22_18.png - - path: output/gsea/study.enplot_CHR10Q23_9.png - - path: output/gsea/study.enplot_CHR10Q24_51.png - - path: output/gsea/study.enplot_CHR10_27.png - - path: output/gsea/study.enplot_CHR11Q23_96.png - - path: output/gsea/study.enplot_CHR12Q13_63.png - - path: output/gsea/study.enplot_CHR12_72.png - - path: output/gsea/study.enplot_CHR14Q32_33.png - - path: output/gsea/study.enplot_CHR14_54.png - - path: output/gsea/study.enplot_CHR15Q24_114.png - - path: output/gsea/study.enplot_CHR16P12_111.png - - path: output/gsea/study.enplot_CHR16Q24_81.png - - path: output/gsea/study.enplot_CHR17Q21_90.png - - path: output/gsea/study.enplot_CHR18P11_36.png - - path: output/gsea/study.enplot_CHR18_60.png - - path: output/gsea/study.enplot_CHR1P22_24.png - - path: output/gsea/study.enplot_CHR1Q21_66.png - - path: output/gsea/study.enplot_CHR20_120.png - - path: output/gsea/study.enplot_CHR21_15.png - - path: output/gsea/study.enplot_CHR22Q12_93.png - - path: output/gsea/study.enplot_CHR22_117.png - - path: output/gsea/study.enplot_CHR2P13_87.png - - path: output/gsea/study.enplot_CHR2P23_69.png - - path: output/gsea/study.enplot_CHR2Q35_108.png - - path: output/gsea/study.enplot_CHR3P14_102.png - - path: output/gsea/study.enplot_CHR3P24_99.png - - path: output/gsea/study.enplot_CHR3Q13_75.png - - path: output/gsea/study.enplot_CHR3Q27_84.png - - path: output/gsea/study.enplot_CHR5Q23_42.png - - path: output/gsea/study.enplot_CHR5Q31_6.png - - path: output/gsea/study.enplot_CHR5Q32_105.png - - path: output/gsea/study.enplot_CHR5_30.png - - path: output/gsea/study.enplot_CHR6Q14_21.png - - path: output/gsea/study.enplot_CHR6_57.png - - path: output/gsea/study.enplot_CHR7P14_78.png - - path: output/gsea/study.enplot_CHR8Q21_3.png - - path: output/gsea/study.enplot_CHR9Q34_45.png - - path: output/gsea/study.enplot_CHR9_48.png - - path: output/gsea/study.enplot_CHRXQ26_12.png - - path: output/gsea/study.gene_set_sizes.tsv - md5sum: 325ff7e37712fc5b6d0a68e55cd545bd - - path: output/gsea/study.global_es_histogram.png - - path: output/gsea/study.gsea_report_for_MUT.html - - path: output/gsea/study.gsea_report_for_MUT.tsv - md5sum: aad1246761d062aa0aeeffb38ec5ff93 - - path: output/gsea/study.gsea_report_for_WT.html - - path: output/gsea/study.gsea_report_for_WT.tsv - md5sum: 7e4f9f158ac88fc9574a8e718cfc1cdc - - path: output/gsea/study.gset_rnd_es_dist_101.png - - path: output/gsea/study.gset_rnd_es_dist_104.png - - path: output/gsea/study.gset_rnd_es_dist_107.png - - path: output/gsea/study.gset_rnd_es_dist_11.png - - path: output/gsea/study.gset_rnd_es_dist_110.png - - path: output/gsea/study.gset_rnd_es_dist_113.png - - path: output/gsea/study.gset_rnd_es_dist_116.png - - path: output/gsea/study.gset_rnd_es_dist_119.png - - path: output/gsea/study.gset_rnd_es_dist_122.png - - path: output/gsea/study.gset_rnd_es_dist_14.png - - path: output/gsea/study.gset_rnd_es_dist_17.png - - path: output/gsea/study.gset_rnd_es_dist_20.png - - path: output/gsea/study.gset_rnd_es_dist_23.png - - path: output/gsea/study.gset_rnd_es_dist_26.png - - path: output/gsea/study.gset_rnd_es_dist_29.png - - path: output/gsea/study.gset_rnd_es_dist_32.png - - path: output/gsea/study.gset_rnd_es_dist_35.png - - path: output/gsea/study.gset_rnd_es_dist_38.png - - path: output/gsea/study.gset_rnd_es_dist_41.png - - path: output/gsea/study.gset_rnd_es_dist_44.png - - path: output/gsea/study.gset_rnd_es_dist_47.png - - path: output/gsea/study.gset_rnd_es_dist_5.png - - path: output/gsea/study.gset_rnd_es_dist_50.png - - path: output/gsea/study.gset_rnd_es_dist_53.png - - path: output/gsea/study.gset_rnd_es_dist_56.png - - path: output/gsea/study.gset_rnd_es_dist_59.png - - path: output/gsea/study.gset_rnd_es_dist_62.png - - path: output/gsea/study.gset_rnd_es_dist_65.png - - path: output/gsea/study.gset_rnd_es_dist_68.png - - path: output/gsea/study.gset_rnd_es_dist_71.png - - path: output/gsea/study.gset_rnd_es_dist_74.png - - path: output/gsea/study.gset_rnd_es_dist_77.png - - path: output/gsea/study.gset_rnd_es_dist_8.png - - path: output/gsea/study.gset_rnd_es_dist_80.png - - path: output/gsea/study.gset_rnd_es_dist_83.png - - path: output/gsea/study.gset_rnd_es_dist_86.png - - path: output/gsea/study.gset_rnd_es_dist_89.png - - path: output/gsea/study.gset_rnd_es_dist_92.png - - path: output/gsea/study.gset_rnd_es_dist_95.png - - path: output/gsea/study.gset_rnd_es_dist_98.png - - path: output/gsea/study.heat_map_1.png - - path: output/gsea/study.heat_map_corr_plot.html - md5sum: 38989738cfe08051a1778208b851f6e9 - - path: output/gsea/study.index.html - - path: output/gsea/study.neg_snapshot.html - md5sum: e6fec17e5497856cf7b48d0d0dde3e3d - - path: output/gsea/study.pos_snapshot.html - md5sum: 4a4961df5c418e8763976f6b62faa805 - - path: output/gsea/study.pvalues_vs_nes_plot.png - - path: output/gsea/study.ranked_gene_list_MUT_versus_WT.tsv - md5sum: 92c560d6d4c562481ef4d2dccafac842 - - path: output/gsea/study.ranked_list_corr_2.png - - path: output/gsea/versions.yml - -- name: gsea gsea test_gsea_gsea_nosets - command: nextflow run ./tests/modules/nf-core/gsea/gsea -entry test_gsea_gsea_nosets -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gsea/gsea/nextflow.config - tags: - - gsea - - gsea/gsea - files: - - path: output/gsea/study.Gsea.rpt - - path: output/gsea/study.butterfly_plot.png - - path: output/gsea/study.gene_set_sizes.tsv - md5sum: 325ff7e37712fc5b6d0a68e55cd545bd - - path: output/gsea/study.global_es_histogram.png - - path: output/gsea/study.gsea_report_for_MUT.html - - path: output/gsea/study.gsea_report_for_MUT.tsv - md5sum: 6e1302d534d278217dec2ad55854f20b - - path: output/gsea/study.gsea_report_for_WT.html - - path: output/gsea/study.gsea_report_for_WT.tsv - md5sum: bf5c56fb5ed060c31a167bda3e7354f3 - - path: output/gsea/study.heat_map_1.png - - path: output/gsea/study.heat_map_corr_plot.html - md5sum: 38989738cfe08051a1778208b851f6e9 - - path: output/gsea/study.index.html - - path: output/gsea/study.neg_snapshot.html - md5sum: ebc73ba6ff13a08e326e2b2aae07096a - - path: output/gsea/study.pos_snapshot.html - md5sum: ebc73ba6ff13a08e326e2b2aae07096a - - path: output/gsea/study.pvalues_vs_nes_plot.png - - path: output/gsea/study.ranked_gene_list_MUT_versus_WT.tsv - md5sum: 92c560d6d4c562481ef4d2dccafac842 - - path: output/gsea/study.ranked_list_corr_2.png - - path: output/gsea/versions.yml - -- name: gsea gsea test_gsea_gsea_zip - command: nextflow run ./tests/modules/nf-core/gsea/gsea -entry test_gsea_gsea_zip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gsea/gsea/nextflow.config - tags: - - gsea - - gsea/gsea - files: - - path: output/gsea/study.Gsea.rpt - - path: output/gsea/study.Gsea.rpt.zip - - path: output/gsea/study.CHR10.html - md5sum: 22919353bea41f7d714d8226482da1e4 - - path: output/gsea/study.CHR10.tsv - md5sum: 73a9336964c5bc78a85f4565a0deb936 - - path: output/gsea/study.CHR10Q21.html - md5sum: 785bf0d2fc2a4cb02f09b840faad92cc - - path: output/gsea/study.CHR10Q21.tsv - md5sum: 7026b101ef8904656c694f6d84d6dce1 - - path: output/gsea/study.CHR10Q21_40.png - - path: output/gsea/study.CHR10Q22.html - md5sum: 026645b0de3a33f0dce387be02d0c674 - - path: output/gsea/study.CHR10Q22.tsv - md5sum: 117663090e727b6b9b5b2f0fc18efaf7 - - path: output/gsea/study.CHR10Q22_19.png - - path: output/gsea/study.CHR10Q23.html - md5sum: 648b1a145ee38a8ad738677246ad4239 - - path: output/gsea/study.CHR10Q23.tsv - md5sum: 3bbd95fda5becfedb275bed0252497b3 - - path: output/gsea/study.CHR10Q23_10.png - - path: output/gsea/study.CHR10Q24.html - md5sum: ee20a6beacfd1f9313f522ce3cd22029 - - path: output/gsea/study.CHR10Q24.tsv - md5sum: 30f70efdd016b85dddfe8f2ac82c8818 - - path: output/gsea/study.CHR10Q24_52.png - - path: output/gsea/study.CHR10_28.png - - path: output/gsea/study.CHR11Q23.html - md5sum: 9a2e7f1a6787cc68e9e0a342431b7614 - - path: output/gsea/study.CHR11Q23.tsv - md5sum: 3d434bb07f5bfe75485313ce691d3b6f - - path: output/gsea/study.CHR11Q23_97.png - - path: output/gsea/study.CHR12.html - md5sum: 156331b5bee99f3855d644c57598c704 - - path: output/gsea/study.CHR12.tsv - md5sum: c59642e40feaebe8740dbedc963395d3 - - path: output/gsea/study.CHR12Q13.html - md5sum: 1e769f3364cffbf86b3845f376b2971f - - path: output/gsea/study.CHR12Q13.tsv - md5sum: 738af83f3d0a0d5ce3487abf2dbea9ca - - path: output/gsea/study.CHR12Q13_64.png - - path: output/gsea/study.CHR12_73.png - - path: output/gsea/study.CHR14.html - md5sum: 164768ee86f5546a3700d72e275644a8 - - path: output/gsea/study.CHR14.tsv - md5sum: 2b91e27831b2650fa84aebcd39c95910 - - path: output/gsea/study.CHR14Q32.html - md5sum: ec08060c3f8409ff277bf4a3c0da9cd1 - - path: output/gsea/study.CHR14Q32.tsv - md5sum: a59ffab651e71d6c6c21eb090452002f - - path: output/gsea/study.CHR14Q32_34.png - - path: output/gsea/study.CHR14_55.png - - path: output/gsea/study.CHR15Q24.html - md5sum: 2c937be23905f4abbdd89a9221b87ed9 - - path: output/gsea/study.CHR15Q24.tsv - md5sum: c3df349a38d4e13f21daee85c49cd727 - - path: output/gsea/study.CHR15Q24_115.png - - path: output/gsea/study.CHR16P12.html - md5sum: 2b473e0db606b01d678058fdb344734c - - path: output/gsea/study.CHR16P12.tsv - md5sum: 2d4b96f20c566208fc129ecb5ddc7def - - path: output/gsea/study.CHR16P12_112.png - - path: output/gsea/study.CHR16Q24.html - md5sum: 6ed25f51b439a18c6ef687b5ad4d747f - - path: output/gsea/study.CHR16Q24.tsv - md5sum: 8068bae266be3f040d55830f3d814623 - - path: output/gsea/study.CHR16Q24_82.png - - path: output/gsea/study.CHR17Q21.html - md5sum: e3b0cf7fac28a00739ca7c00d6e8bd47 - - path: output/gsea/study.CHR17Q21.tsv - md5sum: c1fe27de29f21e3585633579067f633e - - path: output/gsea/study.CHR17Q21_91.png - - path: output/gsea/study.CHR18.html - md5sum: dbab621e91e1f8182b2be5f01439d57c - - path: output/gsea/study.CHR18.tsv - md5sum: aa04a24e5de913dc3879d79b489ab156 - - path: output/gsea/study.CHR18P11.html - md5sum: 2547bf6806442d7800e1cf75272f7cea - - path: output/gsea/study.CHR18P11.tsv - md5sum: a878a99c5a0614e51f048c51a8c8844c - - path: output/gsea/study.CHR18P11_37.png - - path: output/gsea/study.CHR18_61.png - - path: output/gsea/study.CHR1P22.html - md5sum: 0a8ab68e52d6604934b11f45cbc4a9d9 - - path: output/gsea/study.CHR1P22.tsv - md5sum: 630d24e29c17c977637545d55557df5a - - path: output/gsea/study.CHR1P22_25.png - - path: output/gsea/study.CHR1Q21.html - md5sum: 8ae41e08e44cfad7adcd46faf0eed4a0 - - path: output/gsea/study.CHR1Q21.tsv - md5sum: 05a625ffbadcfcb46e2ce7aaaba69f55 - - path: output/gsea/study.CHR1Q21_67.png - - path: output/gsea/study.CHR20.html - md5sum: 7ab53b0e86e6d9e77c63c1a2d2039175 - - path: output/gsea/study.CHR20.tsv - md5sum: ddc1bf49facaf8d2ad83753586e5f38a - - path: output/gsea/study.CHR20_121.png - - path: output/gsea/study.CHR21.html - md5sum: a62c8f2fb79497267638e36a395a1a10 - - path: output/gsea/study.CHR21.tsv - md5sum: 3b513bbfa4e990678bdd6a47003f3941 - - path: output/gsea/study.CHR21_16.png - - path: output/gsea/study.CHR22.html - md5sum: 7dc0cc399d036632c1c72767497cc41b - - path: output/gsea/study.CHR22.tsv - md5sum: 31ef37c7f3610ad803286331f690cbe4 - - path: output/gsea/study.CHR22Q12.html - md5sum: 4dacaae6030467e4eb83c7026b30624c - - path: output/gsea/study.CHR22Q12.tsv - md5sum: cf438ec5cd399de1c6b7ff65deae4307 - - path: output/gsea/study.CHR22Q12_94.png - - path: output/gsea/study.CHR22_118.png - - path: output/gsea/study.CHR2P13.html - md5sum: 3deb087e62e43043e345f30f17474abc - - path: output/gsea/study.CHR2P13.tsv - md5sum: 30064c1421b921c2d69f3451143d45ea - - path: output/gsea/study.CHR2P13_88.png - - path: output/gsea/study.CHR2P23.html - md5sum: 00bc73a37818fc5b6d05122c0c773b81 - - path: output/gsea/study.CHR2P23.tsv - md5sum: de3a0040f744308804e0f57a29129794 - - path: output/gsea/study.CHR2P23_70.png - - path: output/gsea/study.CHR2Q35.html - md5sum: 13f50b1d01ad8d3f669250e3c25c618c - - path: output/gsea/study.CHR2Q35.tsv - md5sum: aad72e817f5373cd12ea11b1acc4577d - - path: output/gsea/study.CHR2Q35_109.png - - path: output/gsea/study.CHR3P14.html - md5sum: 23fcd9ca3527d01c00cb29b2b5f1e3f1 - - path: output/gsea/study.CHR3P14.tsv - md5sum: 9376e3a9b3043d0725780f69a17dd468 - - path: output/gsea/study.CHR3P14_103.png - - path: output/gsea/study.CHR3P24.html - md5sum: 04ac2985e35c3d6db3133b6da097559d - - path: output/gsea/study.CHR3P24.tsv - md5sum: e326b4c1221b19b1ab17feede9e637c6 - - path: output/gsea/study.CHR3P24_100.png - - path: output/gsea/study.CHR3Q13.html - md5sum: d464dce4ebe5b695604ad15d56731a1e - - path: output/gsea/study.CHR3Q13.tsv - md5sum: 8bf0fb21b6ef7e9c67a83dabb8f91fe8 - - path: output/gsea/study.CHR3Q13_76.png - - path: output/gsea/study.CHR3Q27.html - md5sum: 0bf3f1bde949cded670357dda848bacf - - path: output/gsea/study.CHR3Q27.tsv - md5sum: 5d0eb188521981403c0a225e14f25cbe - - path: output/gsea/study.CHR3Q27_85.png - - path: output/gsea/study.CHR5.html - md5sum: a14172ec4cce737c20294222d518bb1a - - path: output/gsea/study.CHR5.tsv - md5sum: 78a09348dada4ded4e2c921bad2ba17c - - path: output/gsea/study.CHR5Q23.html - md5sum: 2a9f47155465c1486795d7513a895e6e - - path: output/gsea/study.CHR5Q23.tsv - md5sum: cf359fb8a320710d2294754abe5dd61b - - path: output/gsea/study.CHR5Q23_43.png - - path: output/gsea/study.CHR5Q31.html - md5sum: d5d3d54cf4c9a76e125ca552f6d7a2e6 - - path: output/gsea/study.CHR5Q31.tsv - md5sum: 144563bca2cdebb9b8cd7e677f41d936 - - path: output/gsea/study.CHR5Q31_7.png - - path: output/gsea/study.CHR5Q32.html - md5sum: 446fae10b9187163f2936715d1d7b2cf - - path: output/gsea/study.CHR5Q32.tsv - md5sum: 212ed9ad35446bc75d56251c23051be5 - - path: output/gsea/study.CHR5Q32_106.png - - path: output/gsea/study.CHR5_31.png - - path: output/gsea/study.CHR6.html - md5sum: b187b1fe265811e702710f4d240c0c42 - - path: output/gsea/study.CHR6.tsv - md5sum: ad9701adf3e508cbeed5b2f6e5534d0c - - path: output/gsea/study.CHR6Q14.html - md5sum: 3315f95af4f834c73e2ee099b7615fc4 - - path: output/gsea/study.CHR6Q14.tsv - md5sum: 468463d60a086cbc7e88d08ede904685 - - path: output/gsea/study.CHR6Q14_22.png - - path: output/gsea/study.CHR6_58.png - - path: output/gsea/study.CHR7P14.html - md5sum: 177d25c4b8615dff187df2ae4a4bd9eb - - path: output/gsea/study.CHR7P14.tsv - md5sum: db965bfea6402110577c9d4fc3dc91e4 - - path: output/gsea/study.CHR7P14_79.png - - path: output/gsea/study.CHR8Q21.html - md5sum: fd6cd66e5c3e128f0ff56da063ad4244 - - path: output/gsea/study.CHR8Q21.tsv - md5sum: 0291f59a2ecb181bbd356fab4d594207 - - path: output/gsea/study.CHR8Q21_4.png - - path: output/gsea/study.CHR9.html - md5sum: b338456b097db4a7cf7fe2eeb29b0052 - - path: output/gsea/study.CHR9.tsv - md5sum: 4e3dad7570a62a11af1d9fbb7481c69a - - path: output/gsea/study.CHR9Q34.html - md5sum: 75ba9004056409c549cb87e9fd8bbdcd - - path: output/gsea/study.CHR9Q34.tsv - md5sum: 1f6e7e63127d79bafe049426c8c1e329 - - path: output/gsea/study.CHR9Q34_46.png - - path: output/gsea/study.CHR9_49.png - - path: output/gsea/study.CHRXQ26.html - md5sum: 78636c92206c543c28f3f41512afb75f - - path: output/gsea/study.CHRXQ26.tsv - md5sum: 5ea132360f57ab160d0f0b5fcc71e52e - - path: output/gsea/study.CHRXQ26_13.png - - path: output/gsea/study.butterfly_plot.png - - path: output/gsea/study.enplot_CHR10Q21_39.png - - path: output/gsea/study.enplot_CHR10Q22_18.png - - path: output/gsea/study.enplot_CHR10Q23_9.png - - path: output/gsea/study.enplot_CHR10Q24_51.png - - path: output/gsea/study.enplot_CHR10_27.png - - path: output/gsea/study.enplot_CHR11Q23_96.png - - path: output/gsea/study.enplot_CHR12Q13_63.png - - path: output/gsea/study.enplot_CHR12_72.png - - path: output/gsea/study.enplot_CHR14Q32_33.png - - path: output/gsea/study.enplot_CHR14_54.png - - path: output/gsea/study.enplot_CHR15Q24_114.png - - path: output/gsea/study.enplot_CHR16P12_111.png - - path: output/gsea/study.enplot_CHR16Q24_81.png - - path: output/gsea/study.enplot_CHR17Q21_90.png - - path: output/gsea/study.enplot_CHR18P11_36.png - - path: output/gsea/study.enplot_CHR18_60.png - - path: output/gsea/study.enplot_CHR1P22_24.png - - path: output/gsea/study.enplot_CHR1Q21_66.png - - path: output/gsea/study.enplot_CHR20_120.png - - path: output/gsea/study.enplot_CHR21_15.png - - path: output/gsea/study.enplot_CHR22Q12_93.png - - path: output/gsea/study.enplot_CHR22_117.png - - path: output/gsea/study.enplot_CHR2P13_87.png - - path: output/gsea/study.enplot_CHR2P23_69.png - - path: output/gsea/study.enplot_CHR2Q35_108.png - - path: output/gsea/study.enplot_CHR3P14_102.png - - path: output/gsea/study.enplot_CHR3P24_99.png - - path: output/gsea/study.enplot_CHR3Q13_75.png - - path: output/gsea/study.enplot_CHR3Q27_84.png - - path: output/gsea/study.enplot_CHR5Q23_42.png - - path: output/gsea/study.enplot_CHR5Q31_6.png - - path: output/gsea/study.enplot_CHR5Q32_105.png - - path: output/gsea/study.enplot_CHR5_30.png - - path: output/gsea/study.enplot_CHR6Q14_21.png - - path: output/gsea/study.enplot_CHR6_57.png - - path: output/gsea/study.enplot_CHR7P14_78.png - - path: output/gsea/study.enplot_CHR8Q21_3.png - - path: output/gsea/study.enplot_CHR9Q34_45.png - - path: output/gsea/study.enplot_CHR9_48.png - - path: output/gsea/study.enplot_CHRXQ26_12.png - - path: output/gsea/study.gene_set_sizes.tsv - md5sum: 325ff7e37712fc5b6d0a68e55cd545bd - - path: output/gsea/study.global_es_histogram.png - - path: output/gsea/study.gsea_report_for_MUT.html - - path: output/gsea/study.gsea_report_for_MUT.tsv - md5sum: aad1246761d062aa0aeeffb38ec5ff93 - - path: output/gsea/study.gsea_report_for_WT.html - - path: output/gsea/study.gsea_report_for_WT.tsv - md5sum: 7e4f9f158ac88fc9574a8e718cfc1cdc - - path: output/gsea/study.gset_rnd_es_dist_101.png - - path: output/gsea/study.gset_rnd_es_dist_104.png - - path: output/gsea/study.gset_rnd_es_dist_107.png - - path: output/gsea/study.gset_rnd_es_dist_11.png - - path: output/gsea/study.gset_rnd_es_dist_110.png - - path: output/gsea/study.gset_rnd_es_dist_113.png - - path: output/gsea/study.gset_rnd_es_dist_116.png - - path: output/gsea/study.gset_rnd_es_dist_119.png - - path: output/gsea/study.gset_rnd_es_dist_122.png - - path: output/gsea/study.gset_rnd_es_dist_14.png - - path: output/gsea/study.gset_rnd_es_dist_17.png - - path: output/gsea/study.gset_rnd_es_dist_20.png - - path: output/gsea/study.gset_rnd_es_dist_23.png - - path: output/gsea/study.gset_rnd_es_dist_26.png - - path: output/gsea/study.gset_rnd_es_dist_29.png - - path: output/gsea/study.gset_rnd_es_dist_32.png - - path: output/gsea/study.gset_rnd_es_dist_35.png - - path: output/gsea/study.gset_rnd_es_dist_38.png - - path: output/gsea/study.gset_rnd_es_dist_41.png - - path: output/gsea/study.gset_rnd_es_dist_44.png - - path: output/gsea/study.gset_rnd_es_dist_47.png - - path: output/gsea/study.gset_rnd_es_dist_5.png - - path: output/gsea/study.gset_rnd_es_dist_50.png - - path: output/gsea/study.gset_rnd_es_dist_53.png - - path: output/gsea/study.gset_rnd_es_dist_56.png - - path: output/gsea/study.gset_rnd_es_dist_59.png - - path: output/gsea/study.gset_rnd_es_dist_62.png - - path: output/gsea/study.gset_rnd_es_dist_65.png - - path: output/gsea/study.gset_rnd_es_dist_68.png - - path: output/gsea/study.gset_rnd_es_dist_71.png - - path: output/gsea/study.gset_rnd_es_dist_74.png - - path: output/gsea/study.gset_rnd_es_dist_77.png - - path: output/gsea/study.gset_rnd_es_dist_8.png - - path: output/gsea/study.gset_rnd_es_dist_80.png - - path: output/gsea/study.gset_rnd_es_dist_83.png - - path: output/gsea/study.gset_rnd_es_dist_86.png - - path: output/gsea/study.gset_rnd_es_dist_89.png - - path: output/gsea/study.gset_rnd_es_dist_92.png - - path: output/gsea/study.gset_rnd_es_dist_95.png - - path: output/gsea/study.gset_rnd_es_dist_98.png - - path: output/gsea/study.heat_map_1.png - - path: output/gsea/study.heat_map_corr_plot.html - md5sum: 38989738cfe08051a1778208b851f6e9 - - path: output/gsea/study.index.html - - path: output/gsea/study.neg_snapshot.html - md5sum: e6fec17e5497856cf7b48d0d0dde3e3d - - path: output/gsea/study.pos_snapshot.html - md5sum: 4a4961df5c418e8763976f6b62faa805 - - path: output/gsea/study.pvalues_vs_nes_plot.png - - path: output/gsea/study.ranked_gene_list_MUT_versus_WT.tsv - md5sum: 92c560d6d4c562481ef4d2dccafac842 - - path: output/gsea/study.ranked_list_corr_2.png - - path: output/gsea/versions.yml