From d0d8b68b3f139cf439b2249359c1f3857df929c5 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 26 Jul 2018 11:16:44 +0200
Subject: [PATCH] bowtie2.nf: improve root finding of index file name as asked
by @elabaron
---
src/nf_modules/Bowtie2/bowtie2.nf | 22 ++++++++++++-------
.../Bowtie2/tests/mapping_paired.nf | 14 ++++++++----
.../Bowtie2/tests/mapping_single.nf | 8 ++++++-
3 files changed, 31 insertions(+), 13 deletions(-)
diff --git a/src/nf_modules/Bowtie2/bowtie2.nf b/src/nf_modules/Bowtie2/bowtie2.nf
index 30b7531..e5cd169 100644
--- a/src/nf_modules/Bowtie2/bowtie2.nf
+++ b/src/nf_modules/Bowtie2/bowtie2.nf
@@ -57,25 +57,31 @@ Channel
.set { index_files }
process mapping_fastq {
- tag "$pair_id"
+ tag "$reads.baseName"
cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
- set pair_id, file(reads) from fastq_files
+ file reads from fastq_files
file index from index_files.toList()
output:
- set pair_id, "*.bam" into bam_files
+ file "*.bam" into bam_files
script:
+ index_id = index[0]
+ for (index_file in index) {
+ if (index_file =~ /.*\.1\.bt2/) {
+ index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+ }
+ }
"""
- bowtie2 --very-sensitive -p ${task.cpus} -x ${index[0].baseName} \
- -1 ${reads[0]} -2 ${reads[1]} 2> \
- ${pair_id}_bowtie2_report.txt | \
- samtools view -Sb - > ${pair_id}.bam
+bowtie2 --very_sensitive -p ${task.cpus} -x ${index_id} \
+-U ${reads} 2> \
+${reads.baseName}_bowtie2_report.txt | \
+samtools view -Sb - > ${reads.baseName}.bam
-if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
+if grep -q "Error" ${reads.baseName}_bowtie2_report.txt; then
exit 1
fi
"""
diff --git a/src/nf_modules/Bowtie2/tests/mapping_paired.nf b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
index 835d0ca..0a16565 100644
--- a/src/nf_modules/Bowtie2/tests/mapping_paired.nf
+++ b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
@@ -26,11 +26,17 @@ process mapping_fastq {
set pair_id, "*.bam" into bam_files
script:
+ index_id = index[0]
+ for (index_file in index) {
+ if (index_file =~ /.*\.1\.bt2/) {
+ index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+ }
+ }
"""
- bowtie2 --very-sensitive -p ${task.cpus} -x ${index[0].baseName} \
- -1 ${reads[0]} -2 ${reads[1]} 2> \
- ${pair_id}_bowtie2_report.txt | \
- samtools view -Sb - > ${pair_id}.bam
+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
if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
exit 1
diff --git a/src/nf_modules/Bowtie2/tests/mapping_single.nf b/src/nf_modules/Bowtie2/tests/mapping_single.nf
index c5c7f58..201c32c 100644
--- a/src/nf_modules/Bowtie2/tests/mapping_single.nf
+++ b/src/nf_modules/Bowtie2/tests/mapping_single.nf
@@ -25,8 +25,14 @@ process mapping_fastq {
file "*.bam" into bam_files
script:
+ index_id = index[0]
+ for (index_file in index) {
+ if (index_file =~ /.*\.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} \
-U ${reads} 2> \
${reads.baseName}_bowtie2_report.txt | \
samtools view -Sb - > ${reads.baseName}.bam
--
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