idx genome mod

src/chipster.nf

@@ -32,7 +32,7 @@ params.genome = "data/tinyTestDataset/*.fasta"
 @type: File
 */
 
-params.idxgenome = ""
+params.idxgenome = "data/tinyTestDataset/*.fasta.fai*"
 /* already indexed reference genome 
 
 @Type: String
@@ -117,13 +117,17 @@ workflow {
       fastqc_preprocessed.out.report
       ).collect()
   )
+
+  mapping_fastq(genome_idx.collect(), fastp_default.out.fastq)
+
   // index reference genome & mapping preprocessed reads
-  if (!params.idxgenome) {
+  /*if (!params.idxgenome) {
     index_fasta(genome_file)
     mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
   } else {
     mapping_fastq(genome_idx.collect(), fastp_default.out.fastq)
   }
+  */
 
   // filter bam - remove reads with quality <30
   filter_bam_quality(mapping_fastq.out.bam)