From 0e7adae3ccb5e020a3f6c40e86fb70308f535da4 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Sat, 20 Feb 2021 08:14:18 +0100
Subject: [PATCH] bwa: replace sambamba by sambools
---
src/.docker_modules/bwa/0.7.17/Dockerfile | 2 +-
src/nf_modules/bwa/main.nf | 3 ++-
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/src/.docker_modules/bwa/0.7.17/Dockerfile b/src/.docker_modules/bwa/0.7.17/Dockerfile
index 0e556121..eaae571b 100644
--- a/src/.docker_modules/bwa/0.7.17/Dockerfile
+++ b/src/.docker_modules/bwa/0.7.17/Dockerfile
@@ -1,4 +1,4 @@
-FROM lbmc/sambamba:0.6.9
+FROM lbmc/samtools:1.11
MAINTAINER Laurent Modolo
ENV BWA_VERSION=0.7.17
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index 38b92512..ada553fe 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -39,7 +39,8 @@ process mapping_fastq {
bwa mem -t ${task.cpus} \
${index_id} ${reads[0]} ${reads[1]} 2> \
${file_id}_bwa_report.txt | \
- sambamba view -S -t ${task.cpus} -f bam - > ${file_id}.bam
+ samtools view -S -t ${task.cpus} -f bam - > ${file_id}.bam
+ samtools view -@ ${task.cpus} -Sb - > ${pair_id}.bam
"""
}
--
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