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

…into add_proteus

CHANGELOG.md

@@ -9,12 +9,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [[#124](https://github.com/nf-core/differentialabundance/pull/124)] - Template update for nf-core/tools v2.8 ([@pinin4fjords](https://github.com/pinin4fjords), review by [@jasmezz](https://github.com/jasmezz))
 - [[#129](https://github.com/nf-core/differentialabundance/pull/129)] - Module updates to fit with recent registry changes ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse), [@adamrtalbot](https://github.com/adamrtalbot))
+- [[#130](https://github.com/nf-core/differentialabundance/pull/130)] - Document reasons for lack of differential expression ([@pinin4fjords](https://github.com/pinin4fjords), review by [@jfy133](https://github.com/jfy133))
+- [[#131](https://github.com/nf-core/differentialabundance/pull/131)] - Improve gtf to table configurability ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
+- [[#137](https://github.com/nf-core/differentialabundance/pull/137)] - Add `--sizefactors_from_controls` and `--gene_id_col` for DESeq2 module to modules.config ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#147](https://github.com/nf-core/differentialabundance/pull/147)] - Add Maxquant analysis module ([@WackerO](https://github.com/WackerO), review by)
 
 ### `Fixed`
 
 - [[#116](https://github.com/nf-core/differentialabundance/issues/116)] - Skip outlier detection with low replication ([@pinin4fjords](https://github.com/pinin4fjords), review by [@nvnieuwk](https://github.com/nvnieuwk))
 - [[#122](https://github.com/nf-core/differentialabundance/pull/126)] - Add spaces to satisfy nf-core download for singularity ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#127](https://github.com/nf-core/differentialabundance/issues/127)] - [Bug] Can't pass samplesheet with -c file.config , or -params-file params.yml or directly with --input samplesheet.csv ([@ctuni](https://github.com/ctuni), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#138 ](https://github.com/nf-core/differentialabundance/issues/138)]- Fix bugs with --control_features and --sizefactors_from_controls ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 
 ## v1.2.0 - 2023-04-19
 

assets/differentialabundance_report.Rmd

@@ -33,6 +33,8 @@ params:
   features_id_col: NULL
   features_name_col: NULL
   features_metadata_cols: NULL 
+  features_gtf_feature_type: NULL
+  features_gtf_table_first_field: NULL
   raw_matrix: null                                            # e.g. 0_salmon.merged.gene_counts.tsv
   normalised_matrix: null
   variance_stabilised_matrix: null                            # e.g. test_files/3_treatment-WT-P23H.vst.tsv
@@ -239,7 +241,7 @@ assay_data <- lapply(assay_files, function(x) {
   colnames(mat) <- observations[[params$observations_name_col]][match(colnames(mat), rownames(observations))]
 
   # Bit hacky, but ensure log
-  if (max(mat, na.rm=T) > 20){
+  if (max(mat) > 20){
     log2(mat+1)
   }else{
     mat 
@@ -320,6 +322,7 @@ differential_results <- lapply(differential_files, function(diff_file){
   }
   
   # Annotate differential tables if possible
+
   if (! is.null(params$features)){
     diff <- merge(features, diff, by.x = params$features_id_col, by.y = params$differential_feature_id_column)
   }

conf/modules.config

@@ -155,9 +155,11 @@ process {
             ]
         ]
         ext.args = { [
+            "--gene_id_col \"${params.features_id_col}\"",
             "--sample_id_col \"${params.observations_id_col}\"",
             "--test $params.deseq2_test",
             "--fit_type $params.deseq2_fit_type",
+            "--sizefactors_from_controls $params.sizefactors_from_controls",
             "--sf_type $params.deseq2_sf_type",
             "--min_replicates_for_replace $params.deseq2_min_replicates_for_replace",
             "--use_t $params.deseq2_use_t",

nextflow.config

@@ -17,7 +17,7 @@ params {
     contrasts                  = null
     matrix                     = null
     control_features           = null
-    sizefactors_from_controls  = null
+    sizefactors_from_controls  = false
 
     // Reporting
     logo_file                  = "${projectDir}/docs/images/nf-core-differentialabundance_logo_light.png"

workflows/differentialabundance.nf

@@ -36,7 +36,7 @@ if (params.study_type == 'affy_array'){
 }
 
 // Check optional parameters
-if (params.control_features) { ch_control_features = file(params.control_features, checkIfExists: true) } else { ch_control_features = [[],[]] }
+if (params.control_features) { ch_control_features = Channel.of([ exp_meta, file(params.control_features, checkIfExists: true)]).first() } else { ch_control_features = [[],[]] }
 if (params.gsea_run) {
     if (params.gsea_gene_sets){
         gene_sets_files = params.gsea_gene_sets.split(",")