src/RNAseq.nf : add adaptor and strand in parameters

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 - \