diff --git a/CHANGELOG.md b/CHANGELOG.md index 63fa9c0f..5667ec0f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,12 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added +- [[#420](https://github.com/nf-core/differentialabundance/pull/420)] - Add missing nf-tests to nf-core modules. ([@nschcolnicov](https://github.com/nschcolnicov), review by [@pinin4fjords](https://github.com/pinin4fjords)) +- [[#380](https://github.com/nf-core/differentialabundance/pull/380)] - Replace local filter_diff_table module with nf-core one, and create nf-tests for tabular_to_gsea_chip. ([@nschcolnicov](https://github.com/nschcolnicov), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#358](https://github.com/nf-core/differentialabundance/pull/358)] - Added software version check in nf-tests and gene biotype column check in `.Rmd` ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#354](https://github.com/nf-core/differentialabundance/pull/354)] - Warning message within the R Markdown report to control when genes don't have annotation data ([@alanmmobbs93](https://github.com/alanmmobbs93)). Review by [@WackerO](https://github.com/WackerO) and [@pinin4fjords](https://github.com/pinin4fjords). - [[#345](https://github.com/nf-core/differentialabundance/pull/345)] - Plot differentially expressed genes by gene biotype ([@atrigila](https://github.com/atrigila), review by [@grst](https://github.com/grst)) - [[#343](https://github.com/nf-core/differentialabundance/pull/343)] - Add pipeline-level nf-tests ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@nschcolnicov](https://github.com/nschcolnicov)) - [[#286](https://github.com/nf-core/differentialabundance/pull/286)] - Integration of limma voom for rnaseq data ([@KamilMaliszArdigen](https://github.com/KamilMaliszArdigen), review by [@pinin4fjords](https://github.com/pinin4fjords)) -- [[#380](https://github.com/nf-core/differentialabundance/pull/380)] - Replace local filter_diff_table module with nf-core one, and create nf-tests for tabular_to_gsea_chip. ([@nschcolnicov](https://github.com/nschcolnicov), review by [@pinin4fjords](https://github.com/pinin4fjords)) ### Fixed diff --git a/modules.json b/modules.json index 23d47cc3..437aed4d 100644 --- a/modules.json +++ b/modules.json @@ -52,7 +52,7 @@ }, "gsea/gsea": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "258399c484a25b880fddc9a8dd35b98f371d31f5", "installed_by": ["modules"] }, "gunzip": { diff --git a/modules/nf-core/gsea/gsea/main.nf b/modules/nf-core/gsea/gsea/main.nf index 6a060c46..2cc542dc 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 f3ce403f..937d3a6a 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 00000000..869cf0ca --- /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 00000000..5ed2fe53 --- /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", + 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