Add additional_allelecounter_flags option to ASCAT (#8644)

Author: SPPearce

modules/nf-core/ascat/main.nf

@@ -40,14 +40,15 @@ process ASCAT {
     def gc_input       = gc_file              ?  "${gc_file}"            : "NULL"
     def rt_input       = rt_file              ?  "${rt_file}"            : "NULL"
 
-    def minCounts_arg                    = args.minCounts                     ?  ", minCounts = ${args.minCounts}"         : ""
-    def bed_file_arg                     = bed_file                           ?  ", BED_file = '${bed_file}'"              : ""
-    def chrom_names_arg                  = args.chrom_names                   ?  ", chrom_names = ${args.chrom_names}"     : ""
-    def min_base_qual_arg                = args.min_base_qual                 ?  ", min_base_qual = ${args.min_base_qual}" : ""
-    def min_map_qual_arg                 = args.min_map_qual                  ?  ", min_map_qual = ${args.min_map_qual}"   : ""
-    def fasta_arg                        = fasta                              ?  ", ref.fasta = '${fasta}'"                : ""
-    def skip_allele_counting_tumour_arg  = args.skip_allele_counting_tumour   ?  ", skip_allele_counting_tumour = ${args.skip_allele_counting_tumour}" : ""
-    def skip_allele_counting_normal_arg  = args.skip_allele_counting_normal   ?  ", skip_allele_counting_normal = ${args.skip_allele_counting_normal}" : ""
+    def minCounts_arg                    = args.minCounts                      ?  ", minCounts = ${args.minCounts}"         : ""
+    def bed_file_arg                     = bed_file                            ?  ", BED_file = '${bed_file}'"              : ""
+    def chrom_names_arg                  = args.chrom_names                    ?  ", chrom_names = ${args.chrom_names}"     : ""
+    def min_base_qual_arg                = args.min_base_qual                  ?  ", min_base_qual = ${args.min_base_qual}" : ""
+    def min_map_qual_arg                 = args.min_map_qual                   ?  ", min_map_qual = ${args.min_map_qual}"   : ""
+    def fasta_arg                        = fasta                               ?  ", ref.fasta = '${fasta}'"                : ""
+    def skip_allele_counting_tumour_arg  = args.skip_allele_counting_tumour    ?  ", skip_allele_counting_tumour = ${args.skip_allele_counting_tumour}"       : ""
+    def skip_allele_counting_normal_arg  = args.skip_allele_counting_normal    ?  ", skip_allele_counting_normal = ${args.skip_allele_counting_normal}"       : ""
+    def additional_allelecounter_arg     = args.additional_allelecounter_flags ?  ", additional_allelecounter_flags = ${args.additional_allelecounter_flags}" : ""
 
     """
     #!/usr/bin/env Rscript
@@ -82,10 +83,10 @@ process ASCAT {
         ${fasta_arg}
         ${skip_allele_counting_tumour_arg}
         ${skip_allele_counting_normal_arg}
+        ${additional_allelecounter_arg}
         , seed = 42
     )
 
-
     # Load the data
     ascat.bc = ascat.loadData(
         Tumor_LogR_file = paste0("${prefix}", ".tumour_tumourLogR.txt"),