From 02fc8ffb53268a6bca8d7ca60b2bb01c03fe1939 Mon Sep 17 00:00:00 2001 From: WackerO Date: Thu, 24 Oct 2024 14:37:35 +0200 Subject: [PATCH 1/6] Added separate param for setting qval threshold for pathway analysis --- assets/RNAseq_report.Rmd | 19 +++++++++++-------- bin/Execute_report.R | 2 ++ modules/local/report.nf | 2 ++ nextflow.config | 1 + nextflow_schema.json | 5 +++++ 5 files changed, 21 insertions(+), 8 deletions(-) diff --git a/assets/RNAseq_report.Rmd b/assets/RNAseq_report.Rmd index 6b78749a..906fcd41 100644 --- a/assets/RNAseq_report.Rmd +++ b/assets/RNAseq_report.Rmd @@ -46,6 +46,7 @@ params: datasources: '' heatmaps_cluster_rows: '' heatmaps_cluster_cols: '' + pathway_pval_threshold: '' #Additional args for the report path_proj_summary: '' @@ -2056,6 +2057,8 @@ if (!isProvided(params$datasources)) { # ------------------ # Set default params # ------------------ +pathway_pval_threshold <- ifelse(params$pathway_pval_threshold == -1, params$adj_pval_threshold, params$pathway_pval_threshold) +pathway_pval_text <- as.character(pathway_pval_threshold) # Set theme for graphs theme_set(theme_classic()) @@ -2094,7 +2097,7 @@ for (file in contrast_files){ correction_method="fdr", sources=datasources, evcodes=TRUE, - user_threshold=params$adj_pval_threshold, + user_threshold=pathway_pval_threshold, custom_bg=custom_background, domain_scope="custom_annotated" ) @@ -2110,7 +2113,7 @@ for (file in contrast_files){ correction_method="fdr", sources=datasources, evcodes=TRUE, - user_threshold=params$adj_pval_threshold, + user_threshold=pathway_pval_threshold, domain_scope="annotated" ) pathway_gostres_nobg <- gostres_nobg$result @@ -2124,7 +2127,7 @@ for (file in contrast_files){ correction_method="fdr", sources=datasources, evcodes=TRUE, - user_threshold=params$adj_pval_threshold, + user_threshold=pathway_pval_threshold, domain_scope="annotated" ) } @@ -2411,7 +2414,7 @@ gost_text, "\n ## Enriched pathways -The plot below summarizes the pathways that were found significantly enriched in DE genes for each contrast (padj value <= ", pval_text, "). +The plot below summarizes the pathways that were found significantly enriched in DE genes for each contrast (padj value <= ", pathway_pval_text, "). Only contrasts for which an enriched pathway was found are shown. Hover over the dots to reveal the pathway names. The table below provides more detail on all enriched pathways.")) ``` @@ -2447,7 +2450,7 @@ if (length(q_list) > 0) { significant=T, correction_method="fdr", sources=datasources, - user_threshold=params$adj_pval_threshold, + user_threshold=pathway_pval_threshold, custom_bg=custom_background, domain_scope="custom_annotated" ) @@ -2457,7 +2460,7 @@ if (length(q_list) > 0) { significant=T, correction_method="fdr", sources=datasources, - user_threshold=params$adj_pval_threshold, + user_threshold=pathway_pval_threshold, domain_scope="annotated" ) } @@ -2470,7 +2473,7 @@ if (length(q_list) > 0) { if (nrow(path_enrich) > 0){ pg2 <- gostplot(gostres, capped=T, interactive=T) - pg2[['x']][['layout']][['annotations']][[1]][['x']] <- -params$adj_pval_threshold + pg2[['x']][['layout']][['annotations']][[1]][['x']] <- -pathway_pval_threshold # limit gostplot y maximum dynamically for all subplots for (counter in c(1:length(contrast_files))) { @@ -2691,7 +2694,7 @@ For pathway analysis, the R packages `gprofiler2 v", version_gprofiler2, " `, `AnnotationDbi v", version_annotation, "` and `", name_species, " v", version_annotation, "` were used. ", database_string, ".\n", -"Pathways were classified as enriched for those genes with an adjusted p-value <= ", pval_text, "." +"Pathways were classified as enriched for those genes with an adjusted p-value <= ", pathway_pval_text, "." )) ``` diff --git a/bin/Execute_report.R b/bin/Execute_report.R index 21d2ad93..8bb51fe8 100755 --- a/bin/Execute_report.R +++ b/bin/Execute_report.R @@ -37,6 +37,7 @@ option_list = list( make_option("--datasources", type="character", default=NULL, help="Which datasources to use for pathway analysis.", metavar="character"), make_option("--heatmaps_cluster_rows", action="store_true", default=FALSE, help="Whether to activate row clustering when generating heatmaps of gene expression in enriched pathways."), make_option("--heatmaps_cluster_cols", action="store_true", default=FALSE, help="Whether to activate column clustering when generating heatmaps of gene expression in enriched pathways."), + make_option("--pathway_pval_threshold", type="double", default=-1, help="Which p value threshold to use for pathway analysis."), make_option(c("-s", "--proj_summary"), type="character", default=NULL, help="Project summary file", metavar="character"), make_option(c("--path_quote"), type="character", default=NULL, help="Path to the quote PDF", metavar="character"), @@ -89,6 +90,7 @@ rmarkdown::render(opt$report, output_file = opt$output, knit_root_dir = wd, outp datasources = opt$datasources, heatmaps_cluster_rows = opt$heatmaps_cluster_rows, heatmaps_cluster_cols = opt$heatmaps_cluster_cols, + pathway_pval_threshold = opt$pathway_pval_threshold, path_proj_summary = opt$proj_summary, path_quote = opt$path_quote, diff --git a/modules/local/report.nf b/modules/local/report.nf index 6164a8ff..f714d5a3 100644 --- a/modules/local/report.nf +++ b/modules/local/report.nf @@ -44,6 +44,7 @@ process REPORT { def datasources_opt = params.datasources ? "--datasources $params.datasources" : '' def heatmaps_cluster_rows_opt = params.heatmaps_cluster_rows ? "--heatmaps_cluster_rows TRUE" : '' def heatmaps_cluster_cols_opt = params.heatmaps_cluster_cols ? "--heatmaps_cluster_cols TRUE" : '' + def pathway_pval_threshold_opt = params.pathway_pval_threshold == -1 ? "--pathway_pval_threshold $params.adj_pval_threshold" : "--pathway_pval_threshold $params.pathway_pval_threshold" def quote_opt = params.quote != 'NO_FILE5' ? "--path_quote $params.quote" : '' @@ -87,6 +88,7 @@ process REPORT { $datasources_opt \ $heatmaps_cluster_rows_opt \ $heatmaps_cluster_cols_opt \ + $pathway_pval_threshold_opt \ $quote_opt \ $software_versions_opt \ --proj_summary $proj_summary \ diff --git a/nextflow.config b/nextflow.config index 175a48af..eea21636 100644 --- a/nextflow.config +++ b/nextflow.config @@ -42,6 +42,7 @@ params { datasources = null heatmaps_cluster_rows = true heatmaps_cluster_cols = false + pathway_pval_threshold = -1 // Additional args for the report project_summary = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 33f48902..672fcf5c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -156,6 +156,11 @@ "type": "boolean", "default": false, "description": "Whether to activate column clustering when generating heatmaps of gene expression in enriched pathways." + }, + "pathway_pval_threshold": { + "type": "number", + "default": -1, + "description": "p value (float) to use as threshold for pathway analysis. If omitted, will use the value of the parameter adj_pval_threshold (default 0.05)." } } }, From 5f23f5468b88006978c9383c21705a15bf0b94ab Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 20 Nov 2024 08:17:34 +0100 Subject: [PATCH 2/6] Fixed pval format in report, added test --- assets/RNAseq_report.Rmd | 2 +- conf/test.config | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/assets/RNAseq_report.Rmd b/assets/RNAseq_report.Rmd index 906fcd41..3f1d849c 100644 --- a/assets/RNAseq_report.Rmd +++ b/assets/RNAseq_report.Rmd @@ -2058,7 +2058,7 @@ if (!isProvided(params$datasources)) { # Set default params # ------------------ pathway_pval_threshold <- ifelse(params$pathway_pval_threshold == -1, params$adj_pval_threshold, params$pathway_pval_threshold) -pathway_pval_text <- as.character(pathway_pval_threshold) +pathway_pval_text <- format(pathway_pval_threshold, scientific=F) # Set theme for graphs theme_set(theme_classic()) diff --git a/conf/test.config b/conf/test.config index 5280f668..72b43194 100644 --- a/conf/test.config +++ b/conf/test.config @@ -28,6 +28,7 @@ params { software_versions = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/software_versions.csv' multiqc = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/MultiQC.zip' run_pathway_analysis = true + pathway_pval_threshold = 0.0003 datasources = 'KEGG,REAC' genome = 'GRCm38' quote = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/offer_example.pdf' From 4c5788210b3de5f7dafbed89488562b087055b9f Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 20 Nov 2024 09:01:47 +0100 Subject: [PATCH 3/6] updated test yml --- tests/test.yml | 18 +++--------------- 1 file changed, 3 insertions(+), 15 deletions(-) diff --git a/tests/test.yml b/tests/test.yml index 11489eb2..78b974a3 100644 --- a/tests/test.yml +++ b/tests/test.yml @@ -68,28 +68,16 @@ - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/gost_pathway_gostplot.png - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/gost_pathway_gostplot.svg - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/pathway_enrichment_results.tsv - md5sum: 92736a4c802ebd4e644682308ecf46dc + md5sum: f0832e1cbdd4cfb4af84740d82a877a3 - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/KEGG_pathway_enrichment_results.tsv - md5sum: 92115e662e0e2489ad05d28f3981fa3a - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/REAC_pathway_enrichment_results.tsv - md5sum: 9077c63139668fd01d3f4086e6acb7bc + md5sum: 29b3ba7ab3ebf9eacc7a021a9b67cdc1 - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/enrichment_plots/KEGG_pathway_enrichment_plot.pdf - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/enrichment_plots/KEGG_pathway_enrichment_plot.png - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/enrichment_plots/REAC_pathway_enrichment_plot.pdf - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/enrichment_plots/REAC_pathway_enrichment_plot.png - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/KEGG_pathways/mmu04360.DE_contrast_condition_genotype_WT_vs_KO.png - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/KEGG_pathways/mmu04360.png - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/KEGG_pathways/mmu04360.xml - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/KEGG_pathways/mmu04610.DE_contrast_condition_genotype_WT_vs_KO.png - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/KEGG_pathways/mmu04610.png - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/KEGG_pathways/mmu04610.xml - path: results_test/pathway_analysis/DE_contrast_condition_treatment_Treated_vs_Control/pathway_enrichment_results.tsv - md5sum: 0a425c10e229bb775597be176c414705 - - path: results_test/pathway_analysis/DE_contrast_condition_treatment_Treated_vs_Control/REAC_pathway_enrichment_results.tsv - md5sum: 6594fdb8c0eb591fa131982a8be00877 - - path: results_test/pathway_analysis/DE_contrast_condition_treatment_Treated_vs_Control/gost_pathway_venn_diagram.pdf - - path: results_test/pathway_analysis/DE_contrast_condition_treatment_Treated_vs_Control/gost_pathway_venn_diagram.png - - path: results_test/pathway_analysis/DE_contrast_condition_treatment_Treated_vs_Control/gost_pathway_venn_diagram.svg - - path: results_test/pathway_analysis/DE_contrast_condition_treatment_Treated_vs_Control/enrichment_plots/REAC_pathway_enrichment_plot.pdf - - path: results_test/pathway_analysis/DE_contrast_condition_treatment_Treated_vs_Control/enrichment_plots/REAC_pathway_enrichment_plot.png + md5sum: 68b329da9893e34099c7d8ad5cb9c940 - path: results_test/RNAseq_report.html From 1e8f63bfcf51bcc4d8c8844f39acf069d3ed5af7 Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 20 Nov 2024 10:19:40 +0100 Subject: [PATCH 4/6] changed test threshold --- conf/test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test.config b/conf/test.config index 72b43194..1761f7d8 100644 --- a/conf/test.config +++ b/conf/test.config @@ -28,7 +28,7 @@ params { software_versions = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/software_versions.csv' multiqc = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/MultiQC.zip' run_pathway_analysis = true - pathway_pval_threshold = 0.0003 + pathway_pval_threshold = 0.0004 datasources = 'KEGG,REAC' genome = 'GRCm38' quote = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/offer_example.pdf' From 90651881e84f484e97711323536c3ad3a8908d04 Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 20 Nov 2024 10:25:48 +0100 Subject: [PATCH 5/6] updated test.yml --- tests/test.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/test.yml b/tests/test.yml index 78b974a3..de207247 100644 --- a/tests/test.yml +++ b/tests/test.yml @@ -73,8 +73,6 @@ md5sum: 29b3ba7ab3ebf9eacc7a021a9b67cdc1 - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/enrichment_plots/KEGG_pathway_enrichment_plot.pdf - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/enrichment_plots/KEGG_pathway_enrichment_plot.png - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/enrichment_plots/REAC_pathway_enrichment_plot.pdf - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/enrichment_plots/REAC_pathway_enrichment_plot.png - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/KEGG_pathways/mmu04610.DE_contrast_condition_genotype_WT_vs_KO.png - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/KEGG_pathways/mmu04610.png - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/KEGG_pathways/mmu04610.xml From f6e4db0461f55090abe8a9a39c4b1dfaf432180b Mon Sep 17 00:00:00 2001 From: WackerO Date: Mon, 2 Dec 2024 08:22:54 +0100 Subject: [PATCH 6/6] renamed param, updated threshold --- CHANGELOG.md | 1 + assets/RNAseq_report.Rmd | 18 +++++++++--------- bin/Execute_report.R | 4 ++-- conf/test.config | 2 +- modules/local/report.nf | 4 ++-- nextflow.config | 2 +- nextflow_schema.json | 4 ++-- 7 files changed, 18 insertions(+), 17 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2c2a9b52..eb67d5f7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added +- [#253](https://github.com/qbic-pipelines/rnadeseq/pull/253) Added separate param for adjusted p-value threshold for gprofiler - [#245](https://github.com/qbic-pipelines/rnadeseq/pull/245) Added background gene list to pathway analysis output ### Changed diff --git a/assets/RNAseq_report.Rmd b/assets/RNAseq_report.Rmd index 3f1d849c..a9305dfe 100644 --- a/assets/RNAseq_report.Rmd +++ b/assets/RNAseq_report.Rmd @@ -46,7 +46,7 @@ params: datasources: '' heatmaps_cluster_rows: '' heatmaps_cluster_cols: '' - pathway_pval_threshold: '' + pathway_adj_pval_threshold: '' #Additional args for the report path_proj_summary: '' @@ -2057,8 +2057,8 @@ if (!isProvided(params$datasources)) { # ------------------ # Set default params # ------------------ -pathway_pval_threshold <- ifelse(params$pathway_pval_threshold == -1, params$adj_pval_threshold, params$pathway_pval_threshold) -pathway_pval_text <- format(pathway_pval_threshold, scientific=F) +pathway_adj_pval_threshold <- ifelse(params$pathway_adj_pval_threshold == -1, params$adj_pval_threshold, params$pathway_adj_pval_threshold) +pathway_pval_text <- format(pathway_adj_pval_threshold, scientific=F) # Set theme for graphs theme_set(theme_classic()) @@ -2097,7 +2097,7 @@ for (file in contrast_files){ correction_method="fdr", sources=datasources, evcodes=TRUE, - user_threshold=pathway_pval_threshold, + user_threshold=pathway_adj_pval_threshold, custom_bg=custom_background, domain_scope="custom_annotated" ) @@ -2113,7 +2113,7 @@ for (file in contrast_files){ correction_method="fdr", sources=datasources, evcodes=TRUE, - user_threshold=pathway_pval_threshold, + user_threshold=pathway_adj_pval_threshold, domain_scope="annotated" ) pathway_gostres_nobg <- gostres_nobg$result @@ -2127,7 +2127,7 @@ for (file in contrast_files){ correction_method="fdr", sources=datasources, evcodes=TRUE, - user_threshold=pathway_pval_threshold, + user_threshold=pathway_adj_pval_threshold, domain_scope="annotated" ) } @@ -2450,7 +2450,7 @@ if (length(q_list) > 0) { significant=T, correction_method="fdr", sources=datasources, - user_threshold=pathway_pval_threshold, + user_threshold=pathway_adj_pval_threshold, custom_bg=custom_background, domain_scope="custom_annotated" ) @@ -2460,7 +2460,7 @@ if (length(q_list) > 0) { significant=T, correction_method="fdr", sources=datasources, - user_threshold=pathway_pval_threshold, + user_threshold=pathway_adj_pval_threshold, domain_scope="annotated" ) } @@ -2473,7 +2473,7 @@ if (length(q_list) > 0) { if (nrow(path_enrich) > 0){ pg2 <- gostplot(gostres, capped=T, interactive=T) - pg2[['x']][['layout']][['annotations']][[1]][['x']] <- -pathway_pval_threshold + pg2[['x']][['layout']][['annotations']][[1]][['x']] <- -pathway_adj_pval_threshold # limit gostplot y maximum dynamically for all subplots for (counter in c(1:length(contrast_files))) { diff --git a/bin/Execute_report.R b/bin/Execute_report.R index 8bb51fe8..7d313bff 100755 --- a/bin/Execute_report.R +++ b/bin/Execute_report.R @@ -37,7 +37,7 @@ option_list = list( make_option("--datasources", type="character", default=NULL, help="Which datasources to use for pathway analysis.", metavar="character"), make_option("--heatmaps_cluster_rows", action="store_true", default=FALSE, help="Whether to activate row clustering when generating heatmaps of gene expression in enriched pathways."), make_option("--heatmaps_cluster_cols", action="store_true", default=FALSE, help="Whether to activate column clustering when generating heatmaps of gene expression in enriched pathways."), - make_option("--pathway_pval_threshold", type="double", default=-1, help="Which p value threshold to use for pathway analysis."), + make_option("--pathway_adj_pval_threshold", type="double", default=-1, help="Which adjusted p value threshold to use for pathway analysis."), make_option(c("-s", "--proj_summary"), type="character", default=NULL, help="Project summary file", metavar="character"), make_option(c("--path_quote"), type="character", default=NULL, help="Path to the quote PDF", metavar="character"), @@ -90,7 +90,7 @@ rmarkdown::render(opt$report, output_file = opt$output, knit_root_dir = wd, outp datasources = opt$datasources, heatmaps_cluster_rows = opt$heatmaps_cluster_rows, heatmaps_cluster_cols = opt$heatmaps_cluster_cols, - pathway_pval_threshold = opt$pathway_pval_threshold, + pathway_adj_pval_threshold = opt$pathway_adj_pval_threshold, path_proj_summary = opt$proj_summary, path_quote = opt$path_quote, diff --git a/conf/test.config b/conf/test.config index 1761f7d8..61abb7b6 100644 --- a/conf/test.config +++ b/conf/test.config @@ -28,7 +28,7 @@ params { software_versions = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/software_versions.csv' multiqc = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/MultiQC.zip' run_pathway_analysis = true - pathway_pval_threshold = 0.0004 + pathway_adj_pval_threshold = 0.0004 datasources = 'KEGG,REAC' genome = 'GRCm38' quote = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/offer_example.pdf' diff --git a/modules/local/report.nf b/modules/local/report.nf index f714d5a3..a67227f9 100644 --- a/modules/local/report.nf +++ b/modules/local/report.nf @@ -44,7 +44,7 @@ process REPORT { def datasources_opt = params.datasources ? "--datasources $params.datasources" : '' def heatmaps_cluster_rows_opt = params.heatmaps_cluster_rows ? "--heatmaps_cluster_rows TRUE" : '' def heatmaps_cluster_cols_opt = params.heatmaps_cluster_cols ? "--heatmaps_cluster_cols TRUE" : '' - def pathway_pval_threshold_opt = params.pathway_pval_threshold == -1 ? "--pathway_pval_threshold $params.adj_pval_threshold" : "--pathway_pval_threshold $params.pathway_pval_threshold" + def pathway_adj_pval_threshold_opt = params.pathway_adj_pval_threshold == -1 ? "--pathway_adj_pval_threshold $params.adj_pval_threshold" : "--pathway_adj_pval_threshold $params.pathway_adj_pval_threshold" def quote_opt = params.quote != 'NO_FILE5' ? "--path_quote $params.quote" : '' @@ -88,7 +88,7 @@ process REPORT { $datasources_opt \ $heatmaps_cluster_rows_opt \ $heatmaps_cluster_cols_opt \ - $pathway_pval_threshold_opt \ + $pathway_adj_pval_threshold_opt \ $quote_opt \ $software_versions_opt \ --proj_summary $proj_summary \ diff --git a/nextflow.config b/nextflow.config index eea21636..b5a13834 100644 --- a/nextflow.config +++ b/nextflow.config @@ -42,7 +42,7 @@ params { datasources = null heatmaps_cluster_rows = true heatmaps_cluster_cols = false - pathway_pval_threshold = -1 + pathway_adj_pval_threshold = -1 // Additional args for the report project_summary = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 672fcf5c..3ee4f42d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -157,10 +157,10 @@ "default": false, "description": "Whether to activate column clustering when generating heatmaps of gene expression in enriched pathways." }, - "pathway_pval_threshold": { + "pathway_adj_pval_threshold": { "type": "number", "default": -1, - "description": "p value (float) to use as threshold for pathway analysis. If omitted, will use the value of the parameter adj_pval_threshold (default 0.05)." + "description": "Adjusted p value (float) to use as threshold for pathway analysis. If omitted, will use the value of the parameter adj_pval_threshold (default 0.05)." } } },