add STAR and HTseq to RNAseq_XGR.nf

src/RNAseq_XGR.nf

@@ -65,7 +65,8 @@ params.fasta = ""
 params.idx = ""
 
 params.fastp_out = "$params.project/fastp/"
-// params.star_mapping_fastq_out = "$params.project/STAR/"
+params.star_mapping_fastq_out = "$params.project/STAR/"
+params.star_index_out = "$params.project/STARindex/"
 
 /*
  ****************************************************************

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

@@ -22,6 +22,9 @@ gffread ${gff3_file} -T -o ${genome_id}.gtf
 process index_with_gtf {
   container = "${container_url}"
   label "big_mem_multi_cpus"
+  if (params.star_index_out != "") {
+    publishDir "results/${params.star_index_out}", mode: 'copy'
+  }
 
   input:
     tuple val(genome_id), path(genome_fasta)