From 5b48bae120dbf14b260a35ebfadaa6ce9f445bfb Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 31 Jul 2018 11:04:01 +0200
Subject: [PATCH] RNAseq_sen1D.nf: mapping process: update to last modification
on upstream
---
src/RNAseq_sen1D.nf | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/RNAseq_sen1D.nf b/src/RNAseq_sen1D.nf
index 5193ff4..30566d9 100644
--- a/src/RNAseq_sen1D.nf
+++ b/src/RNAseq_sen1D.nf
@@ -193,6 +193,7 @@ process index_fasta {
output:
file "*.index*" into index_files
+ file "*_report.txt" into indexing_report
script:
"""
@@ -224,7 +225,7 @@ process mapping_fastq {
script:
index_id = index[0]
for (index_file in index) {
- if (index_file =~ /.*\.1\.ebwt/) {
+ if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
}
}
--
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