diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json old mode 100644 new mode 100755 diff --git a/.editorconfig b/.editorconfig old mode 100644 new mode 100755 diff --git a/.gitattributes b/.gitattributes old mode 100644 new mode 100755 diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml old mode 100644 new mode 100755 diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md old mode 100644 new mode 100755 diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml old mode 100644 new mode 100755 diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml old mode 100644 new mode 100755 diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md old mode 100644 new mode 100755 diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml old mode 100644 new mode 100755 diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml old mode 100644 new mode 100755 diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml old mode 100644 new mode 100755 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml old mode 100644 new mode 100755 index e40f2eb6..ae4653ab --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -40,14 +40,14 @@ jobs: environment.yml - name: Build new docker image if: env.MATCHED_FILES - run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.2 + run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.3dev # Change the version above and the third version below before/after release - name: Pull docker image if: ${{ !env.MATCHED_FILES }} run: | docker pull ghcr.io/qbic-pipelines/rnadeseq:dev - docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.2 + docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.3dev - name: Install Nextflow uses: nf-core/setup-nextflow@v1 @@ -94,14 +94,14 @@ jobs: environment.yml - name: Build new docker image if: env.MATCHED_FILES - run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.2 + run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.3dev # Change the version above and the third version below before/after release - name: Pull docker image if: ${{ !env.MATCHED_FILES }} run: | docker pull ghcr.io/qbic-pipelines/rnadeseq:dev - docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.2 + docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.3dev - name: Install Nextflow uses: nf-core/setup-nextflow@v1 diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml old mode 100644 new mode 100755 diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml old mode 100644 new mode 100755 diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml old mode 100644 new mode 100755 diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml old mode 100644 new mode 100755 diff --git a/.github/workflows/push_github_container_reg.yml b/.github/workflows/push_github_container_reg.yml old mode 100644 new mode 100755 diff --git a/.gitignore b/.gitignore old mode 100644 new mode 100755 diff --git a/.gitpod.yml b/.gitpod.yml old mode 100644 new mode 100755 diff --git a/.nf-core.yml b/.nf-core.yml old mode 100644 new mode 100755 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml old mode 100644 new mode 100755 diff --git a/.prettierignore b/.prettierignore old mode 100644 new mode 100755 diff --git a/.prettierrc.yml b/.prettierrc.yml old mode 100644 new mode 100755 diff --git a/CHANGELOG.md b/CHANGELOG.md old mode 100644 new mode 100755 index 56d1d982..a9e2e139 --- 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 +- [#225](https://github.com/qbic-pipelines/rnadeseq/pull/225) Added param for pathway analysis datasources - [#215](https://github.com/qbic-pipelines/rnadeseq/pull/215) Added gene_name to boxplot titles and filenames; increased threshold before overlapping PCA labels are hidden - [#213](https://github.com/qbic-pipelines/rnadeseq/pull/213) Added smrnaseq input support - [#212](https://github.com/qbic-pipelines/rnadeseq/pull/212) Added computational methods if no --software_versions @@ -17,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed +- [#225](https://github.com/qbic-pipelines/rnadeseq/pull/225) Shortened names of some output files - [#219](https://github.com/qbic-pipelines/rnadeseq/pull/219) Release 2.2 to master - [#220](https://github.com/qbic-pipelines/rnadeseq/pull/220) Commit suggestions from PR review for release 2.2 - [#218](https://github.com/qbic-pipelines/rnadeseq/pull/218) Preparing release 2.2 with version bumps @@ -34,6 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed +- [#225](https://github.com/qbic-pipelines/rnadeseq/pull/225) Fixed too many devices error from tryCatch around normalized heatmaps - [#212](https://github.com/qbic-pipelines/rnadeseq/pull/212) Fixed movability of interactive gostplots - [#208](https://github.com/qbic-pipelines/rnadeseq/pull/208) Fixed relevel bug, the function should now finally work! - [#207](https://github.com/qbic-pipelines/rnadeseq/pull/207) Fixed check of samples in counts vs metadata diff --git a/CITATIONS.md b/CITATIONS.md old mode 100644 new mode 100755 diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md old mode 100644 new mode 100755 diff --git a/Dockerfile b/Dockerfile old mode 100644 new mode 100755 index c13267b3..1a3b6a0f --- a/Dockerfile +++ b/Dockerfile @@ -5,14 +5,14 @@ LABEL org.opencontainers.image.authors="Gisela Gabernet, Alexander Peltzer, Oska LABEL org.opencontainers.image.licenses=MIT COPY environment.yml / #RUN conda install -c conda-forge mamba -RUN mamba env create --file /environment.yml -p /opt/conda/envs/qbic-pipelines-rnadeseq-2.2 && \ +RUN mamba env create --file /environment.yml -p /opt/conda/envs/qbic-pipelines-rnadeseq-2.3dev && \ mamba clean --all --yes RUN apt-get update -qq && \ apt-get install -y zip procps ghostscript # Add conda installation dir to PATH -ENV PATH /opt/conda/envs/qbic-pipelines-rnadeseq-2.2/bin:$PATH +ENV PATH /opt/conda/envs/qbic-pipelines-rnadeseq-2.3dev/bin:$PATH # Dump the details of the installed packates to a file for posterity -RUN mamba env export --name qbic-pipelines-rnadeseq-2.2 > qbic-pipelines-rnadeseq-2.2.yml +RUN mamba env export --name qbic-pipelines-rnadeseq-2.3dev > qbic-pipelines-rnadeseq-2.3dev.yml # Instruct R processes to use these empty files instead of clashing with a local config RUN touch .Rprofile RUN touch .Renviron diff --git a/LICENSE b/LICENSE old mode 100644 new mode 100755 diff --git a/README.md b/README.md old mode 100644 new mode 100755 diff --git a/assets/RNAseq_report.Rmd b/assets/RNAseq_report.Rmd old mode 100644 new mode 100755 index b1aa99b8..ae01a018 --- a/assets/RNAseq_report.Rmd +++ b/assets/RNAseq_report.Rmd @@ -43,6 +43,7 @@ params: custom_gmt: '' set_background: '' custom_background: '' + datasources: '' #Additional args for the report path_proj_summary: '' @@ -168,7 +169,7 @@ isProvided <- function(value) { #this function is used to produce a more informative error message when count table and metadata table disagree write_error_msg <- function(counts, qbicCodes) { error_msg <- "Count table headers do not exactly match the metadata table sample names!\n" - + counts_msg <- "" counts_offending <- "" for (c in names(counts)) { @@ -177,7 +178,7 @@ write_error_msg <- function(counts, qbicCodes) { counts_offending <- paste0(counts_offending, c, "\n") } } - + meta_msg <- "" meta_offending <- "" for (m in qbicCodes) { @@ -398,7 +399,7 @@ if (params$input_type == "smrnaseq") { missing_files <- paste0(substring(missing_files, 1, nchar(missing_files)-2), ".") stop(missing_files, call.=F) } - + # Combine files for later files <- c(hairpin_files, other_files) @@ -528,6 +529,7 @@ DT::datatable(df_QA_neat, options = list(scrollX = "100%", scrollY = "400px", p if (params$input_type %in% c("featurecounts", "smrnaseq")) { cds <- DESeqDataSetFromMatrix( countData =count.table, colData =metadata, design = eval(parse(text=as.character(design[[1]])))) } else if (params$input_type %in% c("rsem", "salmon")) { + ## Create a dataframe which consists of both the gene id and the transcript name gtf <- rtracklayer::import(params$path_gtf) gtf <- as.data.frame(gtf, header=T) @@ -599,7 +601,8 @@ if (params$input_type %in% c("featurecounts", "smrnaseq")) { } } missing_files <- paste0(substring(missing_files, 1, nchar(missing_files)-2), ".") - stop(missing_files, call.=F) } + stop(missing_files, call.=F) + } #The following steps are necessary for the processing of salmon output as the files do # not contain integer counts and can therefore not be directly used for cds @@ -642,6 +645,7 @@ if (params$input_type %in% c("featurecounts", "smrnaseq")) { nm <- assays(cds)[["avgTxLength"]] sf <- estimateSizeFactorsForMatrix(counts(cds)/nm) } + write.table(sf,paste("differential_gene_expression/gene_counts_tables/sizeFactor_libraries.tsv",sep=""), append = FALSE, quote = FALSE, sep = "\t",eol = "\n", na = "NA", dec = ".", row.names = T, col.names = F, qmethod = c("escape", "double")) # Write cds assay table to file @@ -719,7 +723,7 @@ if (run_rlog){ # Cooks distances: get important for example when checking knock-out and overexpression studies pdf("differential_gene_expression/plots/further_diagnostics_plots/Cooks-distances.pdf") par(mar=c(10,3,3,3)) -par( mfrow = c(1,2)) +par(mfrow = c(1,2)) boxplot(log10(assays(cds)[["cooks"]]), range=0, las=2,ylim = c(-15, 15),main="log10-Cooks") boxplot(log2(assays(cds)[["cooks"]]), range=0, las=2,ylim = c(-15, 15),main="log2-Cooks") dev.off() @@ -1052,7 +1056,7 @@ cat(paste0("*** The raw count table and normalized count tables are available [here](./differential_gene_expression/gene_counts_tables). The differential expression analysis is performed using the raw gene count table. -For PCA analysis and heatmap plotting, the `r norm_method_long_text` normalized gene counts were used. +For PCA analysis and heatmap plotting, the `r norm_method_long_text` normalized gene counts were used. `r norm_method_override_text` `r nsub_genes_text` @@ -1348,6 +1352,7 @@ if (isProvided(params$path_contrast_list)) { contrast_names <- append(contrast_names, contname) } } + if (isProvided(params$path_contrast_pairs)) { contrasts <- read.table(path_contrast_pairs, sep="\t", header = T, colClasses = "character") write.table(contrasts, file="differential_gene_expression/metadata/contrast_pairs.tsv", sep="\t", quote=F, col.names = T, row.names = F) @@ -1650,7 +1655,7 @@ if (isProvided(params$path_genelist)) { ggsave(filename=paste("differential_gene_expression/plots/boxplots_requested_genes/",requested_genes_plot_gene_name[i],"_",requested_genes_plot_Ensembl[i],".svg",sep=""), width=10, height=5, plot=plot) ggsave(filename=paste("differential_gene_expression/plots/boxplots_requested_genes/",requested_genes_plot_gene_name[i],"_",requested_genes_plot_Ensembl[i],".png",sep=""), width=10, height=5, plot=plot) ggsave(filename=paste("differential_gene_expression/plots/boxplots_requested_genes/",requested_genes_plot_gene_name[i],"_",requested_genes_plot_Ensembl[i],".pdf",sep=""), width=10, height=5, plot=plot) - } + } } ``` @@ -1717,7 +1722,7 @@ if (isProvided(params$path_genelist)) { ggsave(filename=paste0("differential_gene_expression/plots/boxplots_requested_genes/",requested_genes_plot_gene_name[i],"_",requested_genes_plot_Ensembl[i],"_after_batchcorrect.svg"), width=10, height=5, plot=plot) ggsave(filename=paste0("differential_gene_expression/plots/boxplots_requested_genes/",requested_genes_plot_gene_name[i],"_",requested_genes_plot_Ensembl[i],"_after_batchcorrect.png"), width=10, height=5, plot=plot) ggsave(filename=paste0("differential_gene_expression/plots/boxplots_requested_genes/",requested_genes_plot_gene_name[i],"_",requested_genes_plot_Ensembl[i],"_after_batchcorrect.pdf"), width=10, height=5, plot=plot) - } + } } ``` @@ -1771,8 +1776,12 @@ BiocManager::install(params$species_library, lib=species_dir, version="3.17", fo library(params$species_library, lib.loc=species_dir, character.only=T) species_library_installed <- get(params$species_library) -# gprofiler pathway / term sources parameters -datasources <- c("KEGG", "REAC") +# If provided, prepare datasources from comma-separated string +if (isProvided(params$datasources)) { + datasources <- unlist(strsplit(params$datasources, ',')) +} else { + datasources <- c() +} # Default to 1 for the nb of genes DE in a pathway min_DEG_pathway <- as.integer(params$min_DEG_pathway) @@ -1802,7 +1811,18 @@ mv_status <- F if (isProvided(params$custom_gmt)){ # If custom GMT file was provided, filter it before uploading to use in gost queries (gprofiler will NOT filter itself, so otherwise the output will contain all kinds of datasources, not just the selected ones) - out_gmt <- (Filter(function(line) any(startsWith(line, datasources)), readLines(params$custom_gmt))) + out_gmt <- readLines(params$custom_gmt) + + # If datasources are also provided, filter the GMT + if (isProvided(params$datasources)) { + go_positions <- grep("^GO", datasources) + if (length(go_positions)) { + datasources <- my_vector[-go_positions] # If there are any datasources starting with GO, remove them (gets rid of GO:BP etc.) + datasources <- append(datasources, "GO") # Then add the single entry GO, as otherwise, the filtering might not recognize these datasources + } + out_gmt <- (Filter(function(line) any(startsWith(line, datasources)), out_gmt)) # Remove GMT lines that don't start with a datasource + } + out_path <- paste0(tools::file_path_sans_ext(basename(params$custom_gmt)), "_filtered.gmt") writeLines(out_gmt, out_path) gost_id <- upload_GMT_file(out_path) @@ -1844,6 +1864,11 @@ if (mv_status) { } } +# Set datasources to NULL instead of c() to ensure that the gost queries work +if (!isProvided(params$datasources)) { + datasources <- NULL +} + # ------------------ # Set default params # ------------------ @@ -1859,11 +1884,12 @@ theme_set(theme_classic()) for (file in contrast_files){ - #Reading DE genes list + # Reading DE genes list fname <- tools::file_path_sans_ext(basename(file)) dir.create(paste("pathway_analysis", fname, sep="/")) dir.create(paste("pathway_analysis", fname, "KEGG_pathways", sep="/")) + dir.create(paste("pathway_analysis", fname, "enrichment_plots", sep="/")) DE_genes <- read.csv(file = paste0(path_contrasts, file), sep="\t", header = T) DE_genes <- as.data.frame(DE_genes) @@ -1888,11 +1914,11 @@ for (file in contrast_files){ custom_bg=custom_background, domain_scope="custom_annotated" ) - + pathway_gostres <- gostres$result pathway_gostres <- as.data.frame(pathway_gostres[which(pathway_gostres$significant==TRUE),]) pathway_gostres <- pathway_gostres[which(pathway_gostres$intersection_size>=min_DEG_pathway),] - + # Also run without bg for Venn diagrams gostres_nobg <- gost(query=q, organism=gost_id, @@ -1919,7 +1945,6 @@ for (file in contrast_files){ ) } - # Make data frame of gost result pathway_gostres <- gostres$result @@ -1938,13 +1963,13 @@ for (file in contrast_files){ # Generate non-interactive pathway dotplots in the folder pg <- gostplot(gostres, capped=T, interactive=F) - ggsave(pg, filename = paste0("pathway_analysis", "/", fname, "_gost_pathway_enrichment_plot.pdf"), + ggsave(pg, filename = paste0("pathway_analysis/", "/", fname, "/gost_pathway_gostplot.pdf"), device="pdf", height=10, width=15, units="cm", limitsize=F) - ggsave(pg, filename = paste0("pathway_analysis", "/", fname, "_gost_pathway_enrichment_plot.png"), + ggsave(pg, filename = paste0("pathway_analysis/", "/", fname, "/gost_pathway_gostplot.png"), device="png", height=10, width=15, units="cm", dpi=300, limitsize=F) - ggsave(pg, filename = paste0("pathway_analysis", "/", fname, "_gost_pathway_enrichment_plot.svg"), + ggsave(pg, filename = paste0("pathway_analysis/", "/", fname, "/gost_pathway_gostplot.svg"), device="svg", height=10, width=15, units="cm", dpi=300, limitsize=F) @@ -1958,9 +1983,9 @@ for (file in contrast_files){ no_background=pathway_gostres_nobg$term_name ) pv <- ggvenn::ggvenn(VennInput) - ggsave(paste0("pathway_analysis", "/", fname, "_gost_pathway_venn_diagram.pdf"),pv, device="pdf", width=10, height=15) - ggsave(paste0("pathway_analysis", "/", fname, "_gost_pathway_venn_diagram.png"),pv, device="png", width=10, height=15) - ggsave(paste0("pathway_analysis", "/", fname, "_gost_pathway_venn_diagram.svg"),pv, device="svg", width=10, height=15) + ggsave(paste0("pathway_analysis", "/", fname, "/gost_pathway_venn_diagram.pdf"),pv, device="pdf", width=10, height=15) + ggsave(paste0("pathway_analysis", "/", fname, "/gost_pathway_venn_diagram.png"),pv, device="png", width=10, height=15) + ggsave(paste0("pathway_analysis", "/", fname, "/gost_pathway_venn_diagram.svg"),pv, device="svg", width=10, height=15) } } @@ -1970,7 +1995,7 @@ for (file in contrast_files){ # Save pathway enrichment table in tsv format write.table(pathway_gostres_table, - file = paste0("pathway_analysis", "/", fname, "/", fname, "_pathway_enrichment_results.tsv"), + file = paste0("pathway_analysis", "/", fname, "/pathway_enrichment_results.tsv"), sep="\t", quote = F, col.names = T, row.names = F) print("------------------------------------") @@ -1992,7 +2017,7 @@ for (file in contrast_files){ # Plotting results for df df_subset <- data.frame(Pathway_name = df$short_name, Pathway_code = df$term_id, DE_genes = df$intersection_size, Pathway_size = df$term_size, Fraction_DE = (df$intersection_size / df$term_size), Padj = df$p_value, DE_genes_names = df$intersection) write.table(df_subset, - file = paste0("pathway_analysis", "/", fname, "/", fname, "_", db_source, "_pathway_enrichment_results.tsv"), + file = paste0("pathway_analysis", "/", fname, "/", make.names(db_source), "_pathway_enrichment_results.tsv"), sep="\t", quote = F, col.names = T, row.names = F) # Enriched pathways horizontal barplots of padj values @@ -2004,9 +2029,9 @@ for (file in contrast_files){ scale_fill_continuous(high = "#132B43", low = "#56B1F7") + ggtitle("Enriched pathways") + xlab("") + ylab("Gene fraction (DE genes / Pathway size)") - ggsave(p, filename = paste0("pathway_analysis", "/", fname, "/", fname, "_", db_source, "_pathway_enrichment_plot.pdf"), device = "pdf", height = 5+0.5*nrow(df_subset), units = "cm", limitsize=F) - ggsave(p, filename = paste0("pathway_analysis", "/", fname, "/", fname,"_", db_source, "_pathway_enrichment_plot.png"), device = "png", height = 5+0.5*nrow(df_subset), units = "cm", dpi = 300, limitsize=F) - ggsave(p, filename = paste0("pathway_analysis", "/", fname, "/", fname,"_", db_source, "_pathway_enrichment_plot.svg"), device = "svg", height = 5+0.5*nrow(df_subset), units = "cm", dpi = 300, limitsize=F) + ggsave(p, filename = paste0("pathway_analysis", "/", fname, "/enrichment_plots/", make.names(db_source), "_pathway_enrichment_plot.pdf"), device = "pdf", height = 5+0.5*nrow(df_subset), units = "cm", limitsize=F) + ggsave(p, filename = paste0("pathway_analysis", "/", fname, "/enrichment_plots/", make.names(db_source), "_pathway_enrichment_plot.png"), device = "png", height = 5+0.5*nrow(df_subset), units = "cm", dpi = 300, limitsize=F) + ggsave(p, filename = paste0("pathway_analysis", "/", fname, "/enrichment_plots/", make.names(db_source), "_pathway_enrichment_plot.svg"), device = "svg", height = 5+0.5*nrow(df_subset), units = "cm", dpi = 300, limitsize=F) # Plotting heatmaps and KEGG pathways for all pathways print("Plotting heatmaps...") @@ -2027,38 +2052,39 @@ for (file in contrast_files){ # Skip the heatmaps for CI tests because especially png() works only very unreliably for the heatmaps for some reason if (!isProvided(params$citest) & nrow(mat)>1){ dir.create(paste("pathway_analysis", fname, "pathway_heatmaps", sep="/")) - - # Because the image devices sometimes don't work here, surround them with a tryCatch so that the code continues even if a certain heatmap is not saved + + # Because the image devices sometimes don't work here, surround them with a tryCatch so that the code continues even if a certain heatmap is not saved tryCatch( { - png(filename = paste0("pathway_analysis", "/",fname, "/", "pathway_heatmaps", "/", "Heatmap_normalized_counts_", pathway$source, "_", pathway$term_id, "_",fname, ".png"), width = ifelse(nrow(mat)<=20, 200, 125)+ncol(mat)*40, height = 50+nrow(mat)*50) + png(filename = paste0("pathway_analysis", "/",fname, "/", "pathway_heatmaps", "/", "Heatmap_normalized_counts_", pathway$source, "_", make.names(pathway$term_id), ".png"), width = ifelse(nrow(mat)<=20, 200, 125)+ncol(mat)*40, height = 50+nrow(mat)*50) pheatmap(mat = mat, annotation_col = metadata_save, main = paste("Heatmap of normalized expression values for genes in pathway ", pathway$short_name, "(",pathway$source,")",sep=" "), scale = "row", cluster_cols = F, cluster_rows = T) dev.off() }, error=function(e) { - print(paste0("Could not save Heatmap_normalized_counts_", pathway$source, "_", pathway$term_id, "_",fname, ".png because of the following error:\n", e)) + print(paste0("Could not save pathway_analysis", "/",fname, "/", "pathway_heatmaps", "/", "Heatmap_normalized_counts_", pathway$source, "_", make.names(pathway$term_id), ".png because of the following error:\n", e)) } ) tryCatch( { - pdf(paste0("pathway_analysis", "/", fname, "/", "pathway_heatmaps", "/", "Heatmap_normalized_counts_", pathway$source, "_", pathway$term_id, "_", fname, ".pdf"), width = ifelse(nrow(mat)<=20, 50, 10)+ncol(mat)*0.1, height = 5+nrow(mat)*0.005) + pdf(paste0("pathway_analysis", "/", fname, "/", "pathway_heatmaps", "/", "Heatmap_normalized_counts_", pathway$source, "_", make.names(pathway$term_id), ".pdf"), width = ifelse(nrow(mat)<=20, 50, 10)+ncol(mat)*0.1, height = 5+nrow(mat)*0.005) pheatmap(mat = mat, annotation_col = metadata_save, main = paste("Heatmap of normalized expression values for genes in pathway ", pathway$short_name, "(",pathway$source,")",sep=" "), scale = "row", cluster_cols = F, cluster_rows = T) dev.off() }, error=function(e) { - print(paste0("Could not save Heatmap_normalized_counts_", pathway$source, "_", pathway$term_id, "_", fname, ".pdf because of the following error:\n", e)) + print(paste0("Could not save pathway_analysis", "/", fname, "/", "pathway_heatmaps", "/", "Heatmap_normalized_counts_", pathway$source, "_", make.names(pathway$term_id), ".pdf because of the following error:\n", e)) } ) tryCatch( { - svg(paste0("pathway_analysis", "/", fname, "/", "pathway_heatmaps", "/", "Heatmap_normalized_counts_", pathway$source, "_", pathway$term_id, "_", fname, ".svg"), width = ifelse(nrow(mat)<=20, 50, 10)+ncol(mat)*0.1, height = 5+nrow(mat)*0.005) + svg(paste0("pathway_analysis", "/", fname, "/", "pathway_heatmaps", "/", "Heatmap_normalized_counts_", pathway$source, "_", make.names(pathway$term_id), ".svg"), width = ifelse(nrow(mat)<=20, 50, 10)+ncol(mat)*0.1, height = 5+nrow(mat)*0.005) pheatmap(mat = mat, annotation_col = metadata_save, main = paste("Heatmap of normalized expression values for genes in pathway ", pathway$short_name, "(",pathway$source,")",sep=" "), scale = "row", cluster_cols = F, cluster_rows = T) dev.off() }, error=function(e) { - print(paste0("Could not save Heatmap_normalized_counts_", pathway$source, "_", pathway$term_id, "_", fname, ".svg because of the following error:\n", e)) + print(paste0("Could not save pathway_analysis", "/", fname, "/", "pathway_heatmaps", "/", "Heatmap_normalized_counts_", pathway$source, "_", make.names(pathway$term_id), ".svg because of the following error:\n", e)) } ) + graphics.off() # Close all still open devices from errors. Tried doing this in finally, but that doesn't work } # Plotting pathway view only for kegg pathways @@ -2070,9 +2096,7 @@ for (file in contrast_files){ print_string <- paste0("Plotting pathway: ", pathway_kegg) gene.data = DE_genes gene.data.subset = gene.data[gene.data$Ensembl_ID %in% gene_list, c("Ensembl_ID","log2FoldChange")] - entrez_ids = AnnotationDbi::mapIds(species_library_installed, keys=as.character(gene.data.subset$Ensembl_ID), column = "ENTREZID", keytype=params$keytype, multiVals="first") - gene.data.subset <- gene.data.subset[!(is.na(entrez_ids)),] if (length(entrez_ids)!=length(unique(entrez_ids))) { @@ -2170,9 +2194,11 @@ Inside the pathway analysis results folder, a subfolder for each contrast used f

Expand/collapse - `*_gost_pathway_venn_diagram.pdf/png` - - Venn diagrams showing the numbers of enriched pathways when using a background gene list vs when not using a bg list. -- `*_KEGG_pathway_enrichment_plot.pdf/png` - - Barplots showing the proportion of differentially expressed genes in the pathway. + - Venn diagrams showing the numbers of enriched pathways when using a background gene list vs when not using a bg list. +- `enrichment_plots/*_pathway_enrichment_plot.{pdf/png/svg}` + - Barplots showing the proportion of differentially expressed genes in the pathway for a certain pathway database. +- `gost_pathway_gostplot.{pdf/png/svg}` + - Manhattan plots displaying all enriched pathways. - `KEGG_pathways/` - Contains the KEGG pathways graphs with the log fold change of the differentially expressed genes. - `pathway_heatmaps` @@ -2211,7 +2237,7 @@ names(q_list) <- q_names if (length(q_list) > 0) { #gost query - + if (isProvided(params$set_background)) { gostres <- gost(query=q_list, organism=gost_id, @@ -2422,7 +2448,7 @@ as.character(params$revision), "` pipeline [^5], which was written using the nf-core template [@ewels2020nf]. For differential expression analysis, the read quantification data resulting from `", quant_tool, "` were processed with the R package `DESeq2 v", packageVersion("DESeq2"), -"` [@love2014differential]. The thresholds for differentially expressed genes were set to ", +"` [@love2014differential]. The thresholds for differentially expressed genes were set to ", pval_text, " for the p-value and ", logFC_text, " for the log2 Fold Change." )) @@ -2434,16 +2460,25 @@ name_species = params$species_library version_species = packageVersion(name_species) if (isProvided(params$custom_gmt)){ - database_string <- paste0("Also, a gprofiler query with this custom GMT file was done: `", basename(params$custom_gmt), "`. Entries of the following datasources were considered: ") - dbs <- paste(datasources, collapse="`, `") - database_string <- paste0(database_string, "`", dbs, "`.") -} else { + database_string <- paste0("Also, a gprofiler query with this custom GMT file was done: `", basename(params$custom_gmt), "`.") + + if (isProvided(params$datasources)) { + database_string <- paste(database_string, "Entries of the following datasources were considered: ") + dbs <- paste(datasources, collapse="`, `") + database_string <- paste0(database_string, "`", dbs, "`.") + } else { + database_string <- "" + } + +} else if (isProvided(params$datasources)) { database_string = "Also, the following databases were queried: " database_version_info <- get_version_info(params$organism) database_string <- paste0(database_string, "`gprofiler: ", database_version_info$gprofiler_version, "`") for (db in datasources) { database_string <- paste0(database_string, ", `", db, ": ", database_version_info$sources[[db]]$version, "`") } +} else { + database_string <- paste("All datasources available in g:Profiler were considered (check https://biit.cs.ut.ee/gprofiler/gost and https://biit.cs.ut.ee/gprofiler/page/docs for more info).") } cat(paste0( diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json old mode 100644 new mode 100755 diff --git a/assets/email_template.html b/assets/email_template.html old mode 100644 new mode 100755 diff --git a/assets/email_template.txt b/assets/email_template.txt old mode 100644 new mode 100755 diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml old mode 100644 new mode 100755 diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml old mode 100644 new mode 100755 diff --git a/assets/nf-core-rnadeseq_logo_light.png b/assets/nf-core-rnadeseq_logo_light.png old mode 100644 new mode 100755 diff --git a/assets/references.bibtex b/assets/references.bibtex old mode 100644 new mode 100755 diff --git a/assets/schema_input.json b/assets/schema_input.json old mode 100644 new mode 100755 diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt old mode 100644 new mode 100755 diff --git a/assets/slackreport.json b/assets/slackreport.json old mode 100644 new mode 100755 diff --git a/bin/Execute_report.R b/bin/Execute_report.R index 5b9160d1..cd95b52e 100755 --- a/bin/Execute_report.R +++ b/bin/Execute_report.R @@ -34,6 +34,7 @@ option_list = list( make_option("--set_background", action="store_true", default=TRUE, help="Whether to use a background list for pathway analysis; if true, will only consider expressed genes (i.e. mean counts > 0) for PA."), make_option("--custom_background", type="character", default=NULL, help="Path to a custom background list TXT for pathway analysis; if provided, will only consider genes in that list for PA."), make_option(c("-w", "--min_DEG_pathway"), type="integer", default=NULL, help="min. number of genes DE in a pathway for this pathway to be considered enriched.", metavar="integer"), + make_option("--datasources", type="character", default=NULL, help="Which datasources to use for pathway analysis.", metavar="character"), 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"), @@ -82,6 +83,7 @@ rmarkdown::render(opt$report, output_file = opt$output, knit_root_dir = wd, outp custom_background = opt$custom_background, keytype = opt$keytype, min_DEG_pathway = opt$min_DEG_pathway, + datasources = opt$datasources, path_proj_summary = opt$proj_summary, path_quote = opt$path_quote, diff --git a/conf/base.config b/conf/base.config old mode 100644 new mode 100755 diff --git a/conf/igenomes.config b/conf/igenomes.config old mode 100644 new mode 100755 diff --git a/conf/modules.config b/conf/modules.config old mode 100644 new mode 100755 diff --git a/conf/test.config b/conf/test.config old mode 100644 new mode 100755 diff --git a/conf/test_batcheffect.config b/conf/test_batcheffect.config old mode 100644 new mode 100755 diff --git a/conf/test_contrast_list.config b/conf/test_contrast_list.config old mode 100644 new mode 100755 diff --git a/conf/test_contrast_matrix.config b/conf/test_contrast_matrix.config old mode 100644 new mode 100755 diff --git a/conf/test_custom_gmt.config b/conf/test_custom_gmt.config old mode 100644 new mode 100755 index e3f84934..345c2bef --- a/conf/test_custom_gmt.config +++ b/conf/test_custom_gmt.config @@ -30,4 +30,5 @@ params { run_pathway_analysis = true genome = 'GRCm38' custom_gmt = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/gprofiler_full_mmusculus.ENSG.gmt' + datasources = 'KEGG,REAC' } diff --git a/conf/test_full.config b/conf/test_full.config old mode 100644 new mode 100755 diff --git a/conf/test_no_multiqc.config b/conf/test_no_multiqc.config old mode 100644 new mode 100755 diff --git a/conf/test_relevel.config b/conf/test_relevel.config old mode 100644 new mode 100755 diff --git a/conf/test_smrnaseq.config b/conf/test_smrnaseq.config old mode 100644 new mode 100755 diff --git a/conf/test_star_rsem.config b/conf/test_star_rsem.config old mode 100644 new mode 100755 index 03c11cd5..5e633e22 --- a/conf/test_star_rsem.config +++ b/conf/test_star_rsem.config @@ -27,6 +27,7 @@ params { input_type = 'rsem' run_pathway_analysis = true genome = 'GRCh37' + datasources = 'GO:CC' // species_library = "org.Hs.eg.db" // organism = "hsapiens" // keytype = "ENSEMBL" diff --git a/conf/test_star_salmon.config b/conf/test_star_salmon.config old mode 100644 new mode 100755 diff --git a/conf/test_use_vst.config b/conf/test_use_vst.config old mode 100644 new mode 100755 diff --git a/docs/README.md b/docs/README.md old mode 100644 new mode 100755 diff --git a/docs/images/nf-core-rnadeseq_logo_dark.png b/docs/images/nf-core-rnadeseq_logo_dark.png old mode 100644 new mode 100755 diff --git a/docs/images/nf-core-rnadeseq_logo_light.png b/docs/images/nf-core-rnadeseq_logo_light.png old mode 100644 new mode 100755 diff --git a/docs/output.md b/docs/output.md old mode 100644 new mode 100755 index 99131726..6cc4e044 --- a/docs/output.md +++ b/docs/output.md @@ -52,8 +52,10 @@ If pathway analysis was run, this directory contains the zipped pathway analysis - `*_gost_pathway_venn_diagram.pdf/png` - Venn diagrams showing the numbers of enriched pathways when using a background gene list vs when not using a bg list. -- `*_KEGG_pathway_enrichment_plot.pdf/png` - - Barplots showing the proportion of differentially expressed genes in the pathway. +- `enrichment_plots/*_pathway_enrichment_plot.{pdf/png/svg}` + - Barplots showing the proportion of differentially expressed genes in the pathway for a certain pathway database. +- `gost_pathway_gostplot.{pdf/png/svg}` + - Manhattan plots displaying all enriched pathways. - `KEGG_pathways/` - Contains the KEGG pathways graphs with the log fold change of the differentially expressed genes. - `pathway_heatmaps` diff --git a/docs/usage.md b/docs/usage.md old mode 100644 new mode 100755 diff --git a/environment.yml b/environment.yml old mode 100644 new mode 100755 index cf3dc64d..a9447dcb --- a/environment.yml +++ b/environment.yml @@ -1,7 +1,7 @@ # You can use this file to create a conda environment for this pipeline: # conda env create -f environment.yml # use this to find packages: https://anaconda.org/ -name: qbic-pipelines-rnadeseq-2.2 +name: qbic-pipelines-rnadeseq-2.3dev channels: - bioconda - conda-forge diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar old mode 100644 new mode 100755 diff --git a/main.nf b/main.nf old mode 100644 new mode 100755 diff --git a/modules.json b/modules.json old mode 100644 new mode 100755 diff --git a/modules/local/report.nf b/modules/local/report.nf old mode 100644 new mode 100755 index eac509d0..bc145c70 --- a/modules/local/report.nf +++ b/modules/local/report.nf @@ -1,6 +1,6 @@ process REPORT { - container 'ghcr.io/qbic-pipelines/rnadeseq:2.2' + container 'ghcr.io/qbic-pipelines/rnadeseq:2.3dev' input: path gene_counts @@ -37,6 +37,7 @@ process REPORT { def custom_gmt_opt = custom_gmt.name != 'NO_FILE3' ? "--custom_gmt $custom_gmt" : '' def set_background_opt = params.set_background ? "--set_background TRUE" : "--set_background FALSE" def custom_background_opt = custom_background.name != 'NO_FILE7' ? "--custom_background $custom_background" : '' + def datasources_opt = params.datasources ? "--datasources $params.datasources" : '' def quote_opt = params.quote != 'NO_FILE5' ? "--path_quote $params.quote" : '' def software_versions_opt = params.software_versions != 'NO_FILE6' ? "--software_versions $params.software_versions" : '' @@ -76,6 +77,7 @@ process REPORT { --species_library $params.species_library \ --keytype $params.keytype \ --min_DEG_pathway $params.min_DEG_pathway \ + $datasources_opt \ $quote_opt \ $software_versions_opt \ --proj_summary $proj_summary \ diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf old mode 100644 new mode 100755 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf old mode 100644 new mode 100755 diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml old mode 100644 new mode 100755 diff --git a/nextflow.config b/nextflow.config old mode 100644 new mode 100755 index 9018f037..7397f9c5 --- a/nextflow.config +++ b/nextflow.config @@ -6,6 +6,11 @@ ---------------------------------------------------------------------------------------- */ +// Pin nf-validation to prevent errors from new versions +plugins { + id 'nf-validation@1.1.3' +} + // Global default params, used in configs // params marked with //* exist for the sake of completeness only; // enabling them prevents igenomes from working @@ -39,6 +44,7 @@ params { custom_gmt = 'NO_FILE3' set_background = true custom_background = 'NO_FILE7' + datasources = null // Additional args for the report project_summary = null @@ -252,7 +258,7 @@ manifest { description = """Differential gene expression analysis and pathway analysis of RNAseq data""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.2' + version = '2.3dev' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json old mode 100644 new mode 100755 index adddbf59..d41f8c26 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -125,7 +125,7 @@ }, "custom_gmt": { "type": "string", - "description": "Path to custom GMT file for gost query, this allows e.g. to query older versions of databases for pathway analysis, not necessary if --skip_pathway_analysis = true." + "description": "Path to custom GMT file for gost query, this allows e.g. to query older versions of databases for pathway analysis, not necessary if --skip_pathway_analysis = true. If --datasources is set, the GMT file will be filtered for these datasources." }, "set_background": { "type": "boolean", @@ -140,6 +140,10 @@ "type": "integer", "default": 1, "description": "Integer indicating how many genes in a pathway must be differentially expressed to be considered as enriched, and report these pathways in tables and the final report. The default value is 1." + }, + "datasources": { + "type": "string", + "description": "Which datasources to use for pathway analysis, comma-separated string like 'KEGG,REAC'. See param 'sources' on https://rdrr.io/cran/gprofiler2/man/gost.html for a list of available sources. If not set, will use all sources. If set while a --custom_gmt is provided, will filter the GMT for these datasources (will not filter for the GO subtypes like GO:BP, just for GO)." } } }, diff --git a/pyproject.toml b/pyproject.toml old mode 100644 new mode 100755 diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf old mode 100644 new mode 100755 diff --git a/testdata/MultiQC.zip b/testdata/MultiQC.zip old mode 100644 new mode 100755 diff --git a/testdata/QDESQ/QDESQ_Sample_preparations.tsv b/testdata/QDESQ/QDESQ_Sample_preparations.tsv old mode 100644 new mode 100755 diff --git a/testdata/QDESQ/QDESQ_design.txt b/testdata/QDESQ/QDESQ_design.txt old mode 100644 new mode 100755 diff --git a/testdata/QDESQ/star_rsem/QDESQ081AU.genes.results b/testdata/QDESQ/star_rsem/QDESQ081AU.genes.results old mode 100644 new mode 100755 diff --git a/testdata/QDESQ/star_rsem/QDESQ082A4.genes.results b/testdata/QDESQ/star_rsem/QDESQ082A4.genes.results old mode 100644 new mode 100755 diff --git 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b/testdata/smrnaseq/counts/QABCD00006_mature.sorted.idxstats old mode 100644 new mode 100755 diff --git a/testdata/smrnaseq/counts/QABCD00006_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00006_mature_hairpin.sorted.idxstats old mode 100644 new mode 100755 diff --git a/testdata/smrnaseq/counts/QABCD00007_mature.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00007_mature.sorted.idxstats old mode 100644 new mode 100755 diff --git a/testdata/smrnaseq/counts/QABCD00007_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00007_mature_hairpin.sorted.idxstats old mode 100644 new mode 100755 diff --git a/testdata/smrnaseq/counts/QABCD00008_mature.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00008_mature.sorted.idxstats old mode 100644 new mode 100755 diff --git a/testdata/smrnaseq/counts/QABCD00008_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00008_mature_hairpin.sorted.idxstats old mode 100644 new mode 100755 diff --git a/testdata/smrnaseq/design.txt b/testdata/smrnaseq/design.txt old mode 100644 new mode 100755 diff --git a/testdata/smrnaseq/requested_genes.txt b/testdata/smrnaseq/requested_genes.txt old mode 100644 new mode 100755 diff --git a/testdata/smrnaseq/samplesheet.tsv b/testdata/smrnaseq/samplesheet.tsv old mode 100644 new mode 100755 diff --git a/testdata/software_versions.csv b/testdata/software_versions.csv old mode 100644 new mode 100755 diff --git a/testdata/software_versions_rsem.yml b/testdata/software_versions_rsem.yml old mode 100644 new mode 100755 diff --git a/testdata/software_versions_salmon.yml b/testdata/software_versions_salmon.yml old mode 100644 new mode 100755 diff --git a/testdata/software_versions_smrnaseq.yml b/testdata/software_versions_smrnaseq.yml old mode 100644 new mode 100755 diff --git a/testdata/summary.tsv b/testdata/summary.tsv old mode 100644 new mode 100755 diff --git a/tests/test.yml b/tests/test.yml old mode 100644 new mode 100755 index 56ff217d..585f4a04 --- a/tests/test.yml +++ b/tests/test.yml @@ -60,35 +60,36 @@ - path: results_test/differential_gene_expression/plots/PCA_plot.pdf - path: results_test/differential_gene_expression/plots/PCA_plot.png - path: results_test/differential_gene_expression/plots/PCA_plot.svg - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO_gost_pathway_venn_diagram.pdf - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO_gost_pathway_venn_diagram.png - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO_gost_pathway_venn_diagram.svg - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO_gost_pathway_enrichment_plot.pdf - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO_gost_pathway_enrichment_plot.png - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/DE_contrast_condition_genotype_WT_vs_KO_pathway_enrichment_results.tsv - md5sum: be0f292a205f2ecd453ee27ecdc62615 - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/DE_contrast_condition_genotype_WT_vs_KO_KEGG_pathway_enrichment_results.tsv - md5sum: f0e6d8117e3ff05ddabc3abb98f514b7 - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/DE_contrast_condition_genotype_WT_vs_KO_REAC_pathway_enrichment_results.tsv - md5sum: 3d7616fd0f6cb3aaf9f08252b2bcd223 - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/DE_contrast_condition_genotype_WT_vs_KO_KEGG_pathway_enrichment_plot.pdf - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/DE_contrast_condition_genotype_WT_vs_KO_KEGG_pathway_enrichment_plot.png - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/DE_contrast_condition_genotype_WT_vs_KO_REAC_pathway_enrichment_plot.pdf - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/DE_contrast_condition_genotype_WT_vs_KO_REAC_pathway_enrichment_plot.png + - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/gost_pathway_venn_diagram.pdf + - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/gost_pathway_venn_diagram.png + - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/gost_pathway_venn_diagram.svg + - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/gost_pathway_gostplot.pdf + - 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: 21b907d52008f66f9a85190400fd211e + - 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 + - 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/DE_contrast_condition_treatment_Treated_vs_Control_pathway_enrichment_results.tsv - md5sum: 0bd6dfd32bad6f5292f6cde91f019844 - - path: results_test/pathway_analysis/DE_contrast_condition_treatment_Treated_vs_Control/DE_contrast_condition_treatment_Treated_vs_Control_REAC_pathway_enrichment_results.tsv - md5sum: 452ca5dd8d5f190648988502f85d3ef1 - - 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/DE_contrast_condition_treatment_Treated_vs_Control_REAC_pathway_enrichment_plot.pdf - - path: results_test/pathway_analysis/DE_contrast_condition_treatment_Treated_vs_Control/DE_contrast_condition_treatment_Treated_vs_Control_REAC_pathway_enrichment_plot.png + - path: results_test/pathway_analysis/DE_contrast_condition_treatment_Treated_vs_Control/pathway_enrichment_results.tsv + md5sum: bdc0167b8b33a0da44e34768eead8376 + - 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 - path: results_test/pathway_analysis/heatmap_gene_list/Heatmap_normalized_counts_gene_list.pdf - path: results_test/RNAseq_report.html diff --git a/tests/test_batcheffect.yml b/tests/test_batcheffect.yml old mode 100644 new mode 100755 diff --git a/tests/test_contrast_list.yml b/tests/test_contrast_list.yml old mode 100644 new mode 100755 diff --git a/tests/test_contrast_matrix.yml b/tests/test_contrast_matrix.yml old mode 100644 new mode 100755 diff --git a/tests/test_custom_gmt.yml b/tests/test_custom_gmt.yml old mode 100644 new mode 100755 index 589ccf13..ea161a15 --- a/tests/test_custom_gmt.yml +++ b/tests/test_custom_gmt.yml @@ -60,11 +60,15 @@ - path: results_test/differential_gene_expression/plots/PCA_plot.pdf - path: results_test/differential_gene_expression/plots/PCA_plot.png - path: results_test/differential_gene_expression/plots/PCA_plot.svg - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO_gost_pathway_enrichment_plot.pdf - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO_gost_pathway_enrichment_plot.png - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/DE_contrast_condition_genotype_WT_vs_KO_pathway_enrichment_results.tsv + - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/gost_pathway_gostplot.pdf + - 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/gost_pathway_venn_diagram.pdf + - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/gost_pathway_venn_diagram.png + - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/gost_pathway_venn_diagram.svg + - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO/pathway_enrichment_results.tsv md5sum: eae154d9c7a526cc8c3fcd1a586fa0ed - - path: results_test/pathway_analysis/DE_contrast_condition_treatment_Treated_vs_Control/DE_contrast_condition_treatment_Treated_vs_Control_pathway_enrichment_results.tsv + - path: results_test/pathway_analysis/DE_contrast_condition_treatment_Treated_vs_Control/pathway_enrichment_results.tsv md5sum: bd2cbbf85c3e241743e60b9b8263a31c - path: results_test/pathway_analysis/heatmap_gene_list/Heatmap_normalized_counts_gene_list.pdf - path: results_test/RNAseq_report.html diff --git a/tests/test_full.yml b/tests/test_full.yml old mode 100644 new mode 100755 index c4477cbf..beed5c7d --- a/tests/test_full.yml +++ b/tests/test_full.yml @@ -60,26 +60,26 @@ - path: results_test/differential_gene_expression/plots/PCA_plot.pdf - path: results_test/differential_gene_expression/plots/PCA_plot.png - path: results_test/differential_gene_expression/plots/PCA_plot.svg - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO_gost_pathway_enrichment_plot.pdf - - path: results_test/pathway_analysis/DE_contrast_condition_genotype_WT_vs_KO_gost_pathway_enrichment_plot.png - - path: 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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/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 - path: results_test/pathway_analysis/heatmap_gene_list/Heatmap_normalized_counts_gene_list.pdf - path: results_test/RNAseq_report.html diff --git a/tests/test_no_multiqc.yml b/tests/test_no_multiqc.yml old mode 100644 new mode 100755 diff --git a/tests/test_relevel.yml b/tests/test_relevel.yml old mode 100644 new mode 100755 diff --git a/tests/test_smrnaseq.yml b/tests/test_smrnaseq.yml old mode 100644 new mode 100755 index 34ff104b..39676c01 --- a/tests/test_smrnaseq.yml +++ b/tests/test_smrnaseq.yml @@ -72,18 +72,18 @@ - path: results_test/differential_gene_expression/plots/PCA_plot_with_labels.pdf - path: results_test/differential_gene_expression/plots/PCA_plot_with_labels.png - path: results_test/differential_gene_expression/plots/PCA_plot_with_labels.svg - - path: results_test/pathway_analysis/DE_contrast_condition_treatment_clone9_vs_clone1/DE_contrast_condition_treatment_clone9_vs_clone1_KEGG_pathway_enrichment_plot.pdf - - path: results_test/pathway_analysis/DE_contrast_condition_treatment_clone9_vs_clone1/DE_contrast_condition_treatment_clone9_vs_clone1_KEGG_pathway_enrichment_plot.png - - path: results_test/pathway_analysis/DE_contrast_condition_treatment_clone9_vs_clone1/DE_contrast_condition_treatment_clone9_vs_clone1_KEGG_pathway_enrichment_plot.svg - - path: results_test/pathway_analysis/DE_contrast_condition_treatment_clone9_vs_clone1/DE_contrast_condition_treatment_clone9_vs_clone1_KEGG_pathway_enrichment_results.tsv - md5sum: 2637f5f6f4e74e7723280449e3ac647b - - path: 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