Commit 86d3356e authored by van den Berg's avatar van den Berg
Browse files

Samtools does not utilise the additional threads

parent 5e202f55
......@@ -102,8 +102,6 @@ rule align:
output:
"{sample}/bams/{sample}-{read_group}.sorted.bam"
params:
bwa_threads = 8,
samtools_threads = 3,
compression_level = 1,
rg = "@RG\\tID:{sample}-library-{read_group}\\tSM:{sample}\\tLB:library\\tPL:ILLUMINA"
......@@ -113,12 +111,12 @@ rule align:
container:
containers["bwa-0.7.17-samtools-1.10"]
threads:
11
8
shell:
"set -eo pipefail;"
"bwa mem -t {params.bwa_threads} -R '{params.rg}' {input.ref} "
"bwa mem -t {threads} -R '{params.rg}' {input.ref} "
"{input.r1} {input.r2} 2> {log.bwa} | "
"samtools sort -@ {params.samtools_threads} "
"samtools sort "
"-l {params.compression_level} "
"- -o {output} 2> {log.samtools};"
"samtools index {output}"
......
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