amendments to cutadapt to remove adapters in 5' and 3' from R1 and R2

src/RNAseq_sen1D.nf

@@ -21,22 +21,42 @@ Channel
 
 process adaptor_removal {
   tag "$pair_id"
-  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
 
   input:
   set pair_id, file(reads) from fastq_files
 
   output:
-  set pair_id, "*_cut_R{1,2}_001.fastq.gz" into fastq_files_cut
+  set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
 
   script:
   """
-  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
+  cutadapt -a TGGAATTCTCGGGTGCCAAGG -g CCTTGGCACCCGAGAATTCCA \
+  -o ${pair_id}_cut_R1.fastq.gz \
+  ${reads[0]} > ${pair_id}_report.txt
+
+  cutadapt -a GATCGTCGGACTGTAGAACTCTGAAC -g GTTCAGAGTTCTACAGTCCGACGATC \
+  -o ${pair_id}_cut_R2.fastq.gz \
+  ${reads[1]} > ${pair_id}_report.txt
   """
 }
 
+process 4_random_bases_trimming {
+  tag "$pair_id"
+  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files_cut
+
+  output:
+  set pair_id, "*_cut4_R{1,2}.fastq.gz" into fastq_files_cut
+
+  script:
+  """
+  cutadapt -u 4 -u -4 \
+  -o ${pair_id}_cut4_R1.fastq.gz -p ${pair_id}_cut4_R2.fastq.gz \
+  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+  """
+}
 /*
 * urqt :
 * Imputs : fastq files
@@ -48,22 +68,13 @@ process adaptor_removal {
 * for paired-end data
 */
 
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-
 process trimming {
   tag "${reads}"
   cpus 4
   publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
-  set pair_id, file(reads) from fastq_files_cut
+  set pair_id, file(reads) from fastq_files_cut4
 
   output:
   set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim