From 209416f23b3e730446f8af5ec0ecd7e1a1ab1c25 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 25 Sep 2018 14:10:43 +0200
Subject: [PATCH] SNP_calling.nf: sambamba change tmp dir
---
src/SNP_calling.nf | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/src/SNP_calling.nf b/src/SNP_calling.nf
index 061383f..19b5db1 100644
--- a/src/SNP_calling.nf
+++ b/src/SNP_calling.nf
@@ -138,7 +138,7 @@ sambamba view -t ${task.cpus} -S -f bam -l 0 ${sam} -o ${file_id}.bam
process sort_bam {
tag "$file_id"
- cpus 4
+ cpus 10
input:
set file_id, file(bam) from dedup_bam_files
@@ -148,7 +148,7 @@ process sort_bam {
script:
"""
-sambamba sort -t ${task.cpus} -o ${file_id}_sorted.bam ${bam}
+sambamba sort -t ${task.cpus} --tmpdir=./tmp -o ${file_id}_sorted.bam ${bam}
"""
}
@@ -191,7 +191,7 @@ process index_bam {
script:
"""
-sambamba index -t ${task.cpus} ${bam}
+sambamba index -t ${task.cpus} --tmpdir=./tmp ${bam}
"""
}
@@ -259,3 +259,4 @@ gatk Mutect2 --native-pair-hmm-threads ${task.cpus} -R ${fasta} \
}
+
--
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