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 +2426,7 @@ names(q_list) <- q_names if (length(q_list) > 0) { #gost query - + if (isProvided(params$set_background)) { gostres <- gost(query=q_list, organism=gost_id, @@ -2422,8 +2637,8 @@ as.character(params$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 ", -pval_text, " for the p-value and ", +"` [@love2014differential]. The thresholds for differentially expressed genes were set to ", +pval_text, " for the adjusted p-value and ", logFC_text, " for the log2 Fold Change." )) @@ -2434,16 +2649,25 @@ 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( @@ -2465,7 +2689,7 @@ The following lists all packages used for analysis, together with their versions ```{r versions} sessioninfo::session_info()%>% - details::details(summary = 'Session info/used packages') + details::details(summary = 'Session info/used packages') ``` --- diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json index 99786880..e4fc58d0 100644 --- a/assets/adaptivecard.json +++ b/assets/adaptivecard.json @@ -17,7 +17,7 @@ "size": "Large", "weight": "Bolder", "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", - "text": "nf-core/rnadeseq v${version} - ${runName}", + "text": "qbic-pipelines/rnadeseq v${version} - ${runName}", "wrap": true }, { diff --git a/assets/email_template.html b/assets/email_template.html index 3245bcd4..f93eb897 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -1,111 +1,53 @@ - - - - + + + + - - -
- 
+
+ qbic-pipelines/rnadeseq Pipeline Report
+
+
+
+
+
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
index 04b860b4..b0f33b73 100644
--- a/assets/methods_description_template.yml
+++ b/assets/methods_description_template.yml
@@ -1,13 +1,12 @@
id: "nf-core-rnadeseq-methods-description"
description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
-section_name: "nf-core/rnadeseq Methods Description"
-section_href: "https://github.com/nf-core/rnadeseq"
+section_name: "qbic-pipelines/rnadeseq Methods Description"
+section_href: "https://github.com/qbic-pipelines/rnadeseq"
plot_type: "html"
-## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
## You inject any metadata in the Nextflow '${workflow}' object
data: |
-
- <% if (!success){ out << """
-
-
- <% out << summary.collect{ k,v -> "
-
+
+
+ <% out << summary.collect{ k,v -> "
-
-
+qbic-pipelines/rnadeseq v${version}
-Run Name: $runName
+
-
+ """
+}
+%>
- qbic-pipelines/rnadeseq execution completed unsuccessfully!
+qbic-pipelines/rnadeseq ${version}
+Run Name: $runName
+ +<% if (!success){ + out << """ +
+
- """ } else { out << """
- qbic-pipelines/rnadeseq execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: $exitStatus.
The full error message was:
-${errorReport}
-
+
+ """
+} else {
+ out << """
+ ${errorReport}
+
qbic-pipelines/rnadeseq execution completed successfully!
-
- """ } %>
+ The workflow was completed at $dateComplete (duration: $duration)
-The command used to launch the workflow was as follows:
--$commandLine+
The workflow was completed at $dateComplete (duration: $duration)
+The command used to launch the workflow was as follows:
+$commandLine-
Pipeline Configuration:
-| - $k - | -
- $v- |
-
|---|
Pipeline Configuration:
+| $k | $v |
|---|
qbic-pipelines/rnadeseq
- -qbic-pipelines/rnadeseq
+ + +Methods
-Data was processed using nf-core/rnadeseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
+Data was processed using qbic-pipelines/rnadeseq v${workflow.manifest.version} ${doi_text} adapted from the nf-core workflow template (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:
${workflow.commandLine}${tool_citations}
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 737c3d27..d3a5bdca 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,13 +1,15 @@ report_comment: > - This report has been generated by the qbic-pipelines/rnadeseq + This report has been generated by the qbic-pipelines/rnadeseq analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: + "qbic-pipelines-rnadeseq-methods-description": + order: -1000 software_versions: order: -1001 - "qbic-pipelines-rnadeseq-summary": # this is necessary to prevent a linting error + "qbic-pipelines-rnadeseq-summary": order: -1002 - "qbic-pipelines-rnadeseq-methods-description": - order: -1000 export_plots: true + +disable_version_detection: true diff --git a/assets/schema_input.json b/assets/schema_input.json deleted file mode 100644 index 8f83ef7d..00000000 --- a/assets/schema_input.json +++ /dev/null @@ -1,36 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/master/assets/schema_input.json", - "title": "qbic-pipelines/rnadeseq pipeline - params.input schema", - "description": "Schema for the file provided with params.input", - "type": "array", - "items": { - "type": "object", - "properties": { - "sample": { - "type": "string", - "pattern": "^\\S+$", - "errorMessage": "Sample name must be provided and cannot contain spaces" - }, - "fastq_1": { - "type": "string", - "pattern": "^\\S+\\.f(ast)?q\\.gz$", - "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" - }, - "fastq_2": { - "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", - "anyOf": [ - { - "type": "string", - "pattern": "^\\S+\\.f(ast)?q\\.gz$" - }, - { - "type": "string", - "maxLength": 0 - } - ] - } - }, - "required": ["sample", "fastq_1"] - } -} diff --git a/bin/Execute_report.R b/bin/Execute_report.R index 5b9160d1..574fbc1e 100755 --- a/bin/Execute_report.R +++ b/bin/Execute_report.R @@ -34,6 +34,9 @@ option_list = list( make_option("--set_background", action="store_true", default=TRUE, help="Whether to use a background list for pathway analysis; if true, will only consider expressed genes (i.e. mean counts > 0) for PA."), make_option("--custom_background", type="character", default=NULL, help="Path to a custom background list TXT for pathway analysis; if provided, will only consider genes in that list for PA."), make_option(c("-w", "--min_DEG_pathway"), type="integer", default=NULL, help="min. number of genes DE in a pathway for this pathway to be considered enriched.", metavar="integer"), + make_option("--datasources", type="character", default=NULL, help="Which datasources to use for pathway analysis.", metavar="character"), + make_option("--heatmaps_cluster_rows", action="store_true", default=FALSE, help="Whether to activate row clustering when generating heatmaps of gene expression in enriched pathways."), + make_option("--heatmaps_cluster_cols", action="store_true", default=FALSE, help="Whether to activate column clustering when generating heatmaps of gene expression in enriched pathways."), make_option(c("-s", "--proj_summary"), type="character", default=NULL, help="Project summary file", metavar="character"), make_option(c("--path_quote"), type="character", default=NULL, help="Path to the quote PDF", metavar="character"), @@ -82,6 +85,9 @@ rmarkdown::render(opt$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$datasources, + heatmaps_cluster_rows = opt$heatmaps_cluster_rows, + heatmaps_cluster_cols = opt$heatmaps_cluster_cols, path_proj_summary = opt$proj_summary, path_quote = opt$path_quote, diff --git a/bin/markdown_to_html.r b/bin/markdown_to_html.r deleted file mode 100755 index 212d793c..00000000 --- a/bin/markdown_to_html.r +++ /dev/null @@ -1,51 +0,0 @@ -#!/usr/bin/env Rscript - -# Command line argument processing -args = commandArgs(trailingOnly=TRUE) -if (length(args) < 2) { - stop("Usage: markdown_to_html.r$group
\n" - summary_section += "- \n"
- for (param in group_params.keySet()) {
- summary_section += "
- $param
- ${group_params.get(param) ?: 'N/A'} \n" - } - summary_section += "
$group
\n" + summary_section += "- \n"
+ for (param in group_params.keySet()) {
+ summary_section += "
- $param
- ${group_params.get(param) ?: 'N/A'} \n" + } + summary_section += "