From 8a0dd906bd4a9fe682be390d07af7b29470d1007 Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Tue, 31 Jul 2018 10:22:37 +0200
Subject: [PATCH] change to bowtie1
---
src/RNAseq_sen1D.nf | 28 +++++++++++++++-------------
1 file changed, 15 insertions(+), 13 deletions(-)
diff --git a/src/RNAseq_sen1D.nf b/src/RNAseq_sen1D.nf
index 3b79021..fd47a2d 100644
--- a/src/RNAseq_sen1D.nf
+++ b/src/RNAseq_sen1D.nf
@@ -166,7 +166,7 @@ ${reads[0]} ${reads[1]}
}
/*
-* Bowtie2 :
+* Bowtie1 :
* Imputs : fastq files
* Imputs : fasta files
* Output : bam files
@@ -195,9 +195,9 @@ process index_fasta {
script:
"""
-bowtie2-build --threads ${task.cpus} ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie2_report.txt
+bowtie-build --threads ${task.cpus} -f ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie_report.txt
-if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
+if grep -q "Error" ${fasta.baseName}_bowtie_report.txt; then
exit 1
fi
"""
@@ -210,7 +210,7 @@ fi
process mapping_fastq {
tag "$pair_id"
cpus 4
- publishDir "results/mapping/bams/", mode: 'copy'
+ publishDir "results/mapping_bowtie1/bams/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files_align
@@ -218,22 +218,24 @@ process mapping_fastq {
output:
set pair_id, "*.bam" into bam_files
- file "*_bowtie2_report.txt" into mapping_fastq_report
+ file "*_bowtie1_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]
+ if (index_file =~ /.*\.1\.ebwt/) {
+ index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
}
}
"""
- 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
+# -v specify the max number of missmatch, -k the number of match reported per
+# reads
+bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+-1 ${reads[0]} -2 ${reads[1]} 2> \
+${pair_id}_bowtie_report.txt | \
+samtools view -Sb - > ${pair_id}.bam
+
+if grep -q "Error" ${pair_id}_bowtie_report.txt; then
exit 1
fi
"""
--
GitLab