feat: add clean_raw_counts() param

Author: kelly-sovacool

main.nf

@@ -35,5 +35,5 @@ workflow {
 
     ch_moo = ch_input |
         create_multiOmicDataSet_from_files
-    clean_raw_counts(ch_moo, [ params.aggregate_rows_with_duplicate_gene_names, params.cleanup_column_names, params.split_gene_name ])
+    clean_raw_counts(ch_moo, [ params.aggregate_rows_with_duplicate_gene_names, params.cleanup_column_names, params.split_gene_name, params.gene_name_column_to_use_for_collapsing_duplicates ])
 }

modules/local/mosuite/clean_raw_counts/main.nf

@@ -3,11 +3,11 @@ process clean_raw_counts {
 
     input:
     path(moo)
-    tuple val(aggregate_rows_with_duplicate_gene_names), val(cleanup_column_names), val(split_gene_name)
+    tuple val(aggregate_rows_with_duplicate_gene_names), val(cleanup_column_names), val(split_gene_name), val(gene_column_name_to_use_for_collapsing_duplicates)
 
     output:
     path("moo_clean.rds"), emit: 'moo'
-    path("figures/"), emit: figures
+    path("figures/**"), emit: figures
 
     script:
     """

nextflow.config

@@ -9,6 +9,7 @@ params {
     aggregate_rows_with_duplicate_gene_names = true
     cleanup_column_names = true
     split_gene_name = true
+    gene_name_column_to_use_for_collapsing_duplicates = ''
 
     // Boilerplate options
     outputDir = 'results'