From ca8ad0bb89b640467dc9df9a7d98b01b430d21a6 Mon Sep 17 00:00:00 2001
From: Emmanuel Labaronne <emmanuel.labaronne@ens-lyon.fr>
Date: Mon, 28 Sep 2020 14:17:43 +0200
Subject: [PATCH] src/RNAseq.nf : add adaptor and strand in parameters
---
src/RNAseq.nf | 16 +++++++++-------
1 file changed, 9 insertions(+), 7 deletions(-)
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 9b139c9f..903c1da6 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 - \
--
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