From 22a3597ff7e37cd119c7f9ce6e6955c715b9d2b7 Mon Sep 17 00:00:00 2001
From: lmodolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 30 Jul 2018 15:17:01 +0000
Subject: [PATCH] RNAseq_sen1D.nf: fix bowtie2 index problem
---
src/RNAseq_sen1D.nf | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/src/RNAseq_sen1D.nf b/src/RNAseq_sen1D.nf
index 82493ed..3b79021 100644
--- a/src/RNAseq_sen1D.nf
+++ b/src/RNAseq_sen1D.nf
@@ -221,8 +221,14 @@ process mapping_fastq {
file "*_bowtie2_report.txt" into mapping_fastq_report
script:
+ index_id = index[0]
+ for (index_file in index) {
+ if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/) ) {
+ index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+ }
+ }
"""
- bowtie2 --very-sensitive -p ${task.cpus} -x ${index[0].baseName} \
+ bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
-1 ${reads[0]} -2 ${reads[1]} 2> \
${pair_id}_bowtie2_report.txt | \
samtools view -Sb - > ${pair_id}.bam
--
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