From 654fe7ec5b18c0042c668e8f85aba86f396d248d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 26 Jul 2018 16:08:03 +0200
Subject: [PATCH] Bowtie2: fix bug on nf files
---
src/nf_modules/Bowtie2/bowtie2.nf | 28 ++++++++++++-------
.../Bowtie2/tests/mapping_paired.nf | 1 +
.../Bowtie2/tests/mapping_single.nf | 1 +
3 files changed, 20 insertions(+), 10 deletions(-)
diff --git a/src/nf_modules/Bowtie2/bowtie2.nf b/src/nf_modules/Bowtie2/bowtie2.nf
index e5cd169..9b4203b 100644
--- a/src/nf_modules/Bowtie2/bowtie2.nf
+++ b/src/nf_modules/Bowtie2/bowtie2.nf
@@ -57,16 +57,17 @@ Channel
.set { index_files }
process mapping_fastq {
- tag "$reads.baseName"
+ tag "$pair_id"
cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
- file reads from fastq_files
+ set pair_id, file(reads) from fastq_files
file index from index_files.toList()
output:
- file "*.bam" into bam_files
+ set pair_id, "*.bam" into bam_files
+ file "*_report.txt" into mapping_report
script:
index_id = index[0]
@@ -76,12 +77,12 @@ process mapping_fastq {
}
}
"""
-bowtie2 --very_sensitive -p ${task.cpus} -x ${index_id} \
--U ${reads} 2> \
-${reads.baseName}_bowtie2_report.txt | \
-samtools view -Sb - > ${reads.baseName}.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" ${reads.baseName}_bowtie2_report.txt; then
+if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
exit 1
fi
"""
@@ -116,15 +117,22 @@ process mapping_fastq {
output:
file "*.bam" into bam_files
+ file "*_report.txt" into mapping_report
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
-if grep -q "Error" ${fasta.baseName}_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 0a16565..d102ebb 100644
--- a/src/nf_modules/Bowtie2/tests/mapping_paired.nf
+++ b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
@@ -24,6 +24,7 @@ process mapping_fastq {
output:
set pair_id, "*.bam" into bam_files
+ file "*_report.txt" into mapping_report
script:
index_id = index[0]
diff --git a/src/nf_modules/Bowtie2/tests/mapping_single.nf b/src/nf_modules/Bowtie2/tests/mapping_single.nf
index 201c32c..b96b108 100644
--- a/src/nf_modules/Bowtie2/tests/mapping_single.nf
+++ b/src/nf_modules/Bowtie2/tests/mapping_single.nf
@@ -23,6 +23,7 @@ process mapping_fastq {
output:
file "*.bam" into bam_files
+ file "*_report.txt" into mapping_report
script:
index_id = index[0]
--
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