Add Bowtie 2 parameters to pipeline

src/RNAseq_sen1D.nf

@@ -131,28 +131,13 @@ fi
 * for paired-end data
 */
 
-params.fastq = "$baseDir/data/fastq/trimming/*_trim_{1,2}.fastq.gz"
-params.index = "$baseDir/data/index/*.index.*"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
 process mapping_fastq {
   tag "$pair_id"
   cpus 4
   publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
-  set pair_id, file(reads) from fastq_files
+  set pair_id, file(reads) from fastq_files_trim
   file index from index_files.toList()
 
   output: