Merge branch 'dev' of https://github.com/nf-core/differentialabundance …

…into dev
nf-core · Mar 22, 2024 · a899bb5 · a899bb5
2 parents 2d174ce + 2972621
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diff --git 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`
 
+- [[#254](https://github.com/nf-core/differentialabundance/pull/254)] - Added advanced params section, added QBiC credits ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#250](https://github.com/nf-core/differentialabundance/pull/250)] - Template update for nf-core/tools v2.13.1 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#244](https://github.com/nf-core/differentialabundance/pull/244)] - Add pipeline params for matrixfilter NA options ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#241](https://github.com/nf-core/differentialabundance/pull/241)] - Template update for nf-core/tools v2.13 ([@WackerO](https://github.com/WackerO), review by [@nvnieuwk](https://github.com/nvnieuwk))
@@ -17,7 +18,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [[#240](https://github.com/nf-core/differentialabundance/pull/240) - Publish GSEA reports ([@pinin4fjords](https://github.com/pinin4fjords), review by )
+- [[#254](https://github.com/nf-core/differentialabundance/pull/254)] - Made differential_file_suffix optional ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#240](https://github.com/nf-core/differentialabundance/pull/240)] - Publish GSEA reports ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#231](https://github.com/nf-core/differentialabundance/pull/231)] - Update GSEA module to fix butterfly plot bug ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#226](https://github.com/nf-core/differentialabundance/pull/226)] - Fix DESEQ2_NORM in modules.config ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#221](https://github.com/nf-core/differentialabundance/pull/221)] - Update shinyngs modules to address density plots issue ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))

diff --git a/README.md b/README.md
@@ -110,7 +110,7 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/differentialabundance was originally written by Jonathan Manning ([@pinin4fjords](https://github.com/pinin4fjords)) and Oskar Wacker ([@WackerO](https://github.com/WackerO)). Jonathan Manning (now at Seqera) initially worked on this workflow as an employee of Healx, an AI-powered, patient-inspired tech company, accelerating the discovery and development of treatments for rare diseases. We are grateful for their support of open science in this project.
+nf-core/differentialabundance was originally written by Jonathan Manning ([@pinin4fjords](https://github.com/pinin4fjords)) and Oskar Wacker ([@WackerO](https://github.com/WackerO)). Jonathan Manning (now at Seqera) initially worked on this workflow as an employee of Healx, an AI-powered, patient-inspired tech company, accelerating the discovery and development of treatments for rare diseases. Oskar Wacker works for [QBiC](https://www.qbic.uni-tuebingen.de/) at Tübingen University. We are grateful for the support of open science in this project.
 
 We thank the many members of the nf-core community who assisted with this pipeline, often by reviewing module pull requests including but not limited to:
 

diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd
@@ -360,9 +360,12 @@ treatment-mCherry-hND6-batcheffect.deseq2.results.tsv
 -->
 
 ```{r, echo=FALSE}
-
+differential_file_suffix <- params$differential_file_suffix
+if (is.null(differential_file_suffix)) {
+    differential_file_suffix <- ifelse(params$study_type %in% c('rnaseq'), ".deseq2.results.tsv", ".limma.results.tsv")
+}
 differential_files <- lapply(contrasts$id, function(d){
-    file.path(params$input_dir, paste0(gsub(' |;', '_', d), params$differential_file_suffix))
+    file.path(params$input_dir, paste0(gsub(' |;', '_', d), differential_file_suffix))
 })
 
 differential_results <- lapply(differential_files, function(diff_file){

diff --git a/conf/modules.config b/conf/modules.config
@@ -62,12 +62,11 @@ process {
         ]
         ext.prefix = { "raw." }
         ext.args = { [
-            "--sample_name_col \"${params.observations_name_col}\"",
+            "--sample_name_col \"" + (params.observations_name_col == null ? params.observations_id_col : params.observations_name_col) + "\"",
             "--file_name_col \"${params.affy_file_name_col}\"",
             "--background ${params.affy_background}",
             "--normalize False",
             "--bgversion ${params.affy_bgversion}",
-            "--file_name_col \"${params.affy_file_name_col}\"",
             "--destructive ${params.affy_destructive}",
             "--rm.mask ${params.affy_rm_mask}",
             "--rm.outliers ${params.affy_rm_outliers}",
@@ -86,12 +85,11 @@ process {
         ]
         ext.prefix = { "normalised." }
         ext.args = { [
-            "--sample_name_col \"${params.observations_name_col}\"",
+            "--sample_name_col \"" + (params.observations_name_col == null ? params.observations_id_col : params.observations_name_col) + "\"",
             "--file_name_col \"${params.affy_file_name_col}\"",
             "--background ${params.affy_background}",
             "--normalize True",
             "--bgversion ${params.affy_bgversion}",
-            "--file_name_col \"${params.affy_file_name_col}\"",
             "--destructive ${params.affy_destructive}",
             "--rm.mask ${params.affy_rm_mask}",
             "--rm.outliers ${params.affy_rm_outliers}",
@@ -423,7 +421,7 @@ process {
             "--assay_names \"${params.exploratory_assay_names}\"",
             "--sample_id_col \"${params.observations_id_col}\"",
             "--feature_id_col \"${params.features_id_col}\"",
-            "--feature_name_col \"${params.features_name_col}\"",
+            "--feature_name_col \"" + (params.features_name_col == null ? params.features_id_col : params.features_name_col) + "\"",
             "--diff_feature_id_col \"${params.differential_feature_id_column}\"",
             "--fold_change_column \"${params.differential_fc_column}\"",
             "--pval_column \"${params.differential_pval_column}\"",

diff --git a/nextflow.config b/nextflow.config
@@ -36,7 +36,7 @@ params {
     // Sample sheet options
     observations_type          = 'sample'
     observations_id_col        = 'sample'
-    observations_name_col      = 'sample'
+    observations_name_col      = null
 
     // Feature options
     features                    = null
@@ -89,7 +89,7 @@ params {
     exploratory_palette_name       = 'Set1'
 
     // Differential options
-    differential_file_suffix                = ".deseq2.results.tsv"
+    differential_file_suffix                = null
     differential_feature_id_column          = "gene_id"
     differential_feature_name_column        = "gene_name"
     differential_fc_column                  = "log2FoldChange"

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -80,7 +80,7 @@
                     "type": "string",
                     "fa_icon": "fas fa-border-all",
                     "description": "(RNA-seq only): optional transcript length matrix with samples and genes as the abundance matrix",
-                    "help_text": "if provided, this file willl be used to provide transcript lengths to DESeq2 to model length bias across samples"
+                    "help_text": "If provided, this file willl be used to provide transcript lengths to DESeq2 to model length bias across samples"
                 },
                 "affy_cel_files_archive": {
                     "type": "string",
@@ -119,8 +119,7 @@
                 },
                 "observations_name_col": {
                     "type": "string",
-                    "default": "sample",
-                    "description": "Column in the sample sheet to be used as the display identifier for observations",
+                    "description": "Column in the sample sheet to be used as the display identifier for observations. If unset, will use value of --observations_id_col.",
                     "fa_icon": "fas fa-file-signature"
                 }
             },
@@ -137,13 +136,13 @@
                 "features_id_col": {
                     "type": "string",
                     "default": "gene_id",
-                    "description": "Feature ID attribute in the GTF file (e.g. the gene_id field)",
+                    "description": "Feature ID attribute in the abundance table as well as in the GTF file (e.g. the gene_id field)",
                     "fa_icon": "fas fa-address-card"
                 },
                 "features_name_col": {
                     "type": "string",
                     "default": "gene_name",
-                    "description": "Feature name attribute in the GTF file (e.g. the gene symbol field)",
+                    "description": "Feature name attribute in the abundance table as well as in the GTF file (e.g. the gene symbol field)",
                     "fa_icon": "fas fa-signature"
                 },
                 "features_type": {
@@ -393,7 +392,7 @@
                     "type": "string",
                     "default": "raw,normalised,variance_stabilised",
                     "hidden": true,
-                    "description": "Specifies assay names to be used for matrices, platform-specific",
+                    "description": "Specifies assay names to be used for matrices, platform-specific.",
                     "fa_icon": "fas fa-file-signature"
                 },
                 "exploratory_final_assay": {
@@ -428,8 +427,7 @@
             "properties": {
                 "differential_file_suffix": {
                     "type": "string",
-                    "default": ".deseq2.results.tsv",
-                    "description": "The suffix associated tabular differential results tables",
+                    "description": "Advanced option: the suffix associated tabular differential results tables. Will by default use the appropriate suffix according to the study_type.",
                     "fa_icon": "fas fa-signature"
                 },
                 "differential_feature_id_column": {
@@ -500,7 +498,6 @@
                 }
             },
             "required": [
-                "differential_file_suffix",
                 "differential_feature_id_column",
                 "differential_fc_column",
                 "differential_qval_column",
@@ -1014,6 +1011,7 @@
                 "report_file": {
                     "type": "string",
                     "description": "Rmd report template from which to create the pipeline report",
+                    "help_text": "The pipeline will always generate a default report which gives a good overview of the analysis results. Should this default report not suit your needs, you can provide the path to a custom report instead.",
                     "format": "file-path",
                     "pattern": "^\\S+\\.Rmd$",
                     "fa_icon": "fas fa-book"