Modif RNAseq_XGR.nf to use STAR indexed genome

src/RNAseq_XGR.nf

@@ -31,8 +31,8 @@ def helpMessage() {
 
     References:
       --fasta [path]                  Path to genome fasta file.
-      --genome [path]                 Path to STAR indexed genome. (To avoid the time consumming indexation of "STAR genome generate" step)
       --gtf [path]                    Path to the gtf annotation file.
+      --idx [path]                    Path to the STAR indexed genome (optional). (If allready computed)
 
     Help:                             Display this help message.
       --help

src/nf_modules/star/main_2.7.8a.nf

@@ -194,7 +194,7 @@ process mapping_withindex {
   }
 
   input:
-    tuple val(index_id), path(index)
+    path(index)
     tuple val(reads_id), path(reads) 
 
   output: