diff --git a/src/RNAseq.nf b/src/RNAseq.nf index 9b139c9fad7f61f0033e634a209e8f508cdaa2bd..903c1da659afd7f1f6e1824d7c61b14ca52c8bf4 100644 --- a/src/RNAseq.nf +++ b/src/RNAseq.nf @@ -26,12 +26,14 @@ params.do_fastqc = true params.do_dedup = true params.do_postgenome = true -//////////////////////// -// ADAPTORS SEQUENCES // -//////////////////////// +/////////////////////// +// LIBRARIES OPTIONS // +/////////////////////// params.adaptorR1 = "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA" params.adaptorR2 = "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT" +params.strand = "FR" + ////////////// // LOG INFO // @@ -137,8 +139,8 @@ process trimming { script: """ cutadapt -j ${task.cpus} \ - -a "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA" \ - -A "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT" \ + -a ${params.adaptorR1} \ + -A ${params.adaptorR2} \ -o ${file_id}_tmp_R1.fastq.gz \ -p ${file_id}_tmp_R2.fastq.gz \ --minimum-length 70 \ @@ -285,7 +287,7 @@ hisat2 -x ${index_id} \ -1 ${fastq_filtred[0]} \ -2 ${fastq_filtred[1]} \ --un-conc-gz ${file_id}_notaligned_R%.fastq.gz \ - --rna-strandness 'FR' \ + --rna-strandness ${params.strand} \ --dta \ 2> ${file_id}_genome.txt \ | samtools view -bS -F 4 - \ @@ -466,7 +468,7 @@ hisat2 -x ${index2_id} \ -p ${task.cpus} \ -1 ${fastq_unaligned[0]} \ -2 ${fastq_unaligned[1]} \ - --rna-strandness 'FR' \ + --rna-strandness ${params.strand} \ --dta\ 2> ${file_id}_postgenome.txt \ | samtools view -bS -F 4 - \