create RNASeq.nf

src/RNASeq.nf

+log.info "fastq files : ${params.fastq}"
+
+Channel
+  .fromFilePairs( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+
+process adaptor_removal {
+  tag "$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}.fastq.gz" into fastq_files_cut
+
+  script:
+  """
+  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
+  """
+}

src/fasta_sampler.nf

@@ -9,7 +9,7 @@ process sample_fasta {
 file fasta from fasta_file
 
   output:
-file "sample.fasta" into fasta_sample
+file "*_sample.fasta" into fasta_sample
 
   script:
 """