From 9a8ff6096494fd04a4556559d7829a5b80d90f53 Mon Sep 17 00:00:00 2001 From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr> Date: Tue, 31 Jul 2018 14:15:35 +0200 Subject: [PATCH] correction bowtie 2 --- src/RNAseq_sen1D_bowtie2.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/RNAseq_sen1D_bowtie2.nf b/src/RNAseq_sen1D_bowtie2.nf index 3b79021..3671747 100644 --- a/src/RNAseq_sen1D_bowtie2.nf +++ b/src/RNAseq_sen1D_bowtie2.nf @@ -214,7 +214,7 @@ process mapping_fastq { input: set pair_id, file(reads) from fastq_files_align - file index from index_files.toList() + file index from index_files.collect() output: set pair_id, "*.bam" into bam_files @@ -228,7 +228,7 @@ process mapping_fastq { } } """ - bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \ + bowtie2 --very-sensitive --fr -p ${task.cpus} -x ${index_id} \ -1 ${reads[0]} -2 ${reads[1]} 2> \ ${pair_id}_bowtie2_report.txt | \ samtools view -Sb - > ${pair_id}.bam -- GitLab