From ff9f90af736446733debfe858cc2131543730098 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 30 Jul 2018 17:27:32 +0200
Subject: [PATCH] Bowti2: modify index handle to better deal with weird file
names
---
src/nf_modules/Bowtie2/bowtie2.nf | 4 ++--
src/nf_modules/Bowtie2/tests/mapping_paired.nf | 2 +-
src/nf_modules/Bowtie2/tests/mapping_single.nf | 2 +-
3 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/Bowtie2/bowtie2.nf b/src/nf_modules/Bowtie2/bowtie2.nf
index 18c1479..8ec01cc 100644
--- a/src/nf_modules/Bowtie2/bowtie2.nf
+++ b/src/nf_modules/Bowtie2/bowtie2.nf
@@ -72,7 +72,7 @@ process mapping_fastq {
script:
index_id = index[0]
for (index_file in index) {
- if (index_file =~ /.*\.1\.bt2/) {
+ if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
}
}
@@ -122,7 +122,7 @@ process mapping_fastq {
script:
index_id = index[0]
for (index_file in index) {
- if (index_file =~ /.*\.1\.bt2/) {
+ if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
}
}
diff --git a/src/nf_modules/Bowtie2/tests/mapping_paired.nf b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
index d102ebb..4cacca4 100644
--- a/src/nf_modules/Bowtie2/tests/mapping_paired.nf
+++ b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
@@ -29,7 +29,7 @@ process mapping_fastq {
script:
index_id = index[0]
for (index_file in index) {
- if (index_file =~ /.*\.1\.bt2/) {
+ if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
}
}
diff --git a/src/nf_modules/Bowtie2/tests/mapping_single.nf b/src/nf_modules/Bowtie2/tests/mapping_single.nf
index 568a68e..19f491a 100644
--- a/src/nf_modules/Bowtie2/tests/mapping_single.nf
+++ b/src/nf_modules/Bowtie2/tests/mapping_single.nf
@@ -28,7 +28,7 @@ process mapping_fastq {
script:
index_id = index[0]
for (index_file in index) {
- if (index_file =~ /.*\.1\.bt2/) {
+ if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
}
}
--
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