RNASEQ.nf miy fo paid nd

src/RNASeq.nf

@@ -8,36 +8,37 @@
 
 
 /*
-* for single-end data
+* for paired-end data
 */
 
-params.fastq = "$baseDir/data/fastq/*.fastq"
+params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
 
 log.info "fastq files : ${params.fastq}"
 
 Channel
-  .fromPath( params.fastq )
+  .fromFilePairs( params.fastq )
   .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
   .set { fastq_files }
 
 process adaptor_removal {
-  tag "$reads.baseName"
+  tag "$pair_id"
   publishDir "results/fastq/adaptor_removal/", mode: 'copy'
 
   input:
-  file reads from fastq_files
+  set pair_id, file(reads) from fastq_files
 
   output:
-  file "*_cut.fastq.gz" into fastq_files_cut
+  file "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
 
   script:
   """
-  cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT\
-  -o ${reads.baseName}_cut.fastq.gz \
-  ${reads} > ${reads.baseName}_report.txt
+  cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
+  -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
+  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
   """
 }
 
+
 /*
 * urqt :
 * Imputs : fastq files