From ec41d5e0a84e2eedd047a9e3201995ecc7e974c2 Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Wed, 18 Jul 2018 14:31:36 +0000
Subject: [PATCH] modify params.fastq to include the .gz format and modify the
output to include _001 and include the 5' adapter
---
"src/RNAseq sen1\342\210\206.nf" | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git "a/src/RNAseq sen1\342\210\206.nf" "b/src/RNAseq sen1\342\210\206.nf"
index 8695b03..eda4e8a 100644
--- "a/src/RNAseq sen1\342\210\206.nf"
+++ "b/src/RNAseq sen1\342\210\206.nf"
@@ -10,7 +10,7 @@
* for paired-end data
*/
-params.fastq = "$baseDir/data/fastq/*_R{1,2}_001.fastq"
+params.fastq = "$baseDir/data/fastq/*_R{1,2}_001.fastq.gz"
log.info "fastq files : ${params.fastq}"
@@ -27,11 +27,11 @@ process adaptor_removal {
set pair_id, file(reads) from fastq_files
output:
- set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+ set pair_id, "*_cut_R{1,2}_001.fastq.gz" into fastq_files_cut
script:
"""
- cutadapt -a TGGAATTCTCGGGTGCCAAGG -g CCTTGGCACCCGAGAATTCCA -A TGGAATTCTCGGGTGCCAAGG -G CCTTGGCACCCGAGAATTCCA \
+ 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
"""
--
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