Harmonize the feature name columns params

CHANGELOG.md

@@ -61,6 +61,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [[#646](https://github.com/nf-core/differentialabundance/pull/646)] - Remove the `--differential_feature_name_column` parameter and consolidate its functionality into `--features_name_col` ([@delfiterradas](https://github.com/delfiterradas), review by [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)).
 - [[#652](https://github.com/nf-core/differentialabundance/pull/652)] - Harmonize `--contrasts` and `--contrasts_yml` ([@atrigila](https://github.com/atrigila), review by [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)).
 - [[#626](https://github.com/nf-core/differentialabundance/pull/626)] - Update documentation, bump Nextflow version, `versions.yml` output cleanup and add params_yaml to report bundle ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila), [@apeltzer](https://github.com/apeltzer), [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)).
 - [[#628](https://github.com/nf-core/differentialabundance/pull/628)] - Removed `--deseq2_cores` parameter and infer from task cpus instead,([@delfiterradas](https://github.com/delfiterradas), review by [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)).

assets/differentialabundance_report.qmd

@@ -1174,9 +1174,9 @@ foo <- lapply(names(p_value_types), function(pvt) {
 
             # Determine which column to use for labels
             if (!is.null(params$meta$params$features) &&
-                !is.null(params$meta$params$differential_feature_name_column) &&
-                (params$meta$params$differential_feature_name_column %in% colnames(differential_results[[1]]))) {
-                label_col <- params$meta$params$differential_feature_name_column
+                !is.null(params$meta$params$features_name_col) &&
+                (params$meta$params$features_name_col %in% colnames(differential_results[[1]]))) {
+                label_col <- params$meta$params$features_name_col
             } else {
                 label_col <- params$meta$params$differential_feature_id_column
             }
@@ -1258,9 +1258,9 @@ for (i in 1:nrow(contrasts)) {
 
     # Labels: prefer feature name if present
     if (!is.null(params$features) &&
-        !is.null(params$meta$params$differential_feature_name_column) &&
-        (params$meta$params$differential_feature_name_column %in% colnames(full_de))) {
-        label_col <- params$meta$params$differential_feature_name_column
+        !is.null(params$meta$params$features_name_col) &&
+        (params$meta$params$features_name_col %in% colnames(full_de))) {
+        label_col <- params$meta$params$features_name_col
     } else {
         label_col <- params$meta$params$differential_feature_id_column
     }

conf/paramsheet.yaml

@@ -7,7 +7,6 @@
   features_name_col: gene_name
   features_metadata_cols: gene_id,gene_name,gene_biotype
   differential_feature_id_column: gene_id
-  differential_feature_name_column: gene_name
 
   observations_id_col: sample
   observations_name_col: sample
@@ -111,7 +110,6 @@
   differential_pval_column: P.Value
   differential_qval_column: adj.P.Val
   differential_feature_id_column: PROBEID
-  differential_feature_name_column: SYMBOL
 
   shinyngs_build_app: true
 
@@ -145,7 +143,6 @@
   differential_pval_column: P.Value
   differential_qval_column: adj.P.Val
   differential_feature_id_column: ID
-  differential_feature_name_column: Symbol
 
 - paramset_name: limma_maxquant
   differential_method: limma
@@ -167,7 +164,6 @@
   differential_pval_column: P.Value
   differential_qval_column: adj.P.Val
   differential_feature_id_column: Majority protein IDs
-  differential_feature_name_column: Majority protein IDs
 
   proteus_measurecol_prefix: LFQ intensity
 

nextflow.config

@@ -90,7 +90,6 @@ params {
     differential_method                     = 'deseq2'  // 'deseq2', 'limma', 'dream'
     differential_file_suffix                = null
     differential_feature_id_column          = "gene_id"
-    differential_feature_name_column        = "gene_name"
     differential_fc_column                  = "log2FoldChange"
     differential_pval_column                = "pvalue"
     differential_qval_column                = "padj"

nextflow_schema.json

@@ -557,12 +557,6 @@
                     "description": "Maximum q value used to calculate differential feature numbers",
                     "fa_icon": "fas fa-angle-double-up"
                 },
-                "differential_feature_name_column": {
-                    "type": "string",
-                    "default": "gene_name",
-                    "description": "Where a features file (GTF) has been provided, what attribute to use to name features",
-                    "fa_icon": "fas fa-signature"
-                },
                 "differential_foldchanges_logged": {
                     "type": "boolean",
                     "default": true,