modify params.fastq to include the .gz format and modify the output to include...

modify params.fastq to include the .gz format and modify the output to include _001 and include the 5' adapter

src/RNAseq sen1∆.nf

@@ -10,7 +10,7 @@
 * for paired-end data
 */
 
-params.fastq = "$baseDir/data/fastq/*_R{1,2}_001.fastq"
+params.fastq = "$baseDir/data/fastq/*_R{1,2}_001.fastq.gz"
 
 log.info "fastq files : ${params.fastq}"
 
@@ -27,11 +27,11 @@ process adaptor_removal {
   set pair_id, file(reads) from fastq_files
 
   output:
-  set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+  set pair_id, "*_cut_R{1,2}_001.fastq.gz" into fastq_files_cut
 
   script:
   """
-  cutadapt -a TGGAATTCTCGGGTGCCAAGG -g CCTTGGCACCCGAGAATTCCA -A TGGAATTCTCGGGTGCCAAGG -G CCTTGGCACCCGAGAATTCCA \
+  cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GTTCAGAGTTCTACAGTCCGACGATC \
   -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
   ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
   """