Commit 5e202f55 authored by van den Berg's avatar van den Berg
Browse files

Revert "Switch to bwa version 2"

This reverts commit 0cf92f4b.

bwa-mem2 can crash when multiple processes are running on the same
system. See https://github.com/bwa-mem2/bwa-mem2/issues/88 for details.
parent 1ad2f17f
......@@ -111,12 +111,12 @@ rule align:
bwa = "log/{sample}/align.{read_group}.bwa.log",
samtools = "log/{sample}/align.{read_group}.samtools.log"
container:
containers["bwa2-2.0-samtools-1.10"]
containers["bwa-0.7.17-samtools-1.10"]
threads:
11
shell:
"set -eo pipefail;"
"bwa-mem2 mem -t {params.bwa_threads} -R '{params.rg}' {input.ref} "
"bwa mem -t {params.bwa_threads} -R '{params.rg}' {input.ref} "
"{input.r1} {input.r2} 2> {log.bwa} | "
"samtools sort -@ {params.samtools_threads} "
"-l {params.compression_level} "
......
......@@ -7,7 +7,7 @@ containers = {
'bcftools': 'docker://quay.io/biocontainers/bcftools:1.9--ha228f0b_4',
'bedtools-2.26-python-2.7': 'docker://quay.io/biocontainers/mulled-v2-3251e6c49d800268f0bc575f28045ab4e69475a6:4ce073b219b6dabb79d154762a9b67728c357edb-0',
'biopet-scatterregions': 'docker://quay.io/biocontainers/biopet-scatterregions:0.2--0',
'bwa2-2.0-samtools-1.10': 'docker://quay.io/biocontainers/mulled-v2-6a15c99309c82b345497d24489bee67bbb76c2f6:1c9c3227b9bf825a8dc9726a25701aa23c0b1f12-0',
'bwa-0.7.17-samtools-1.10': 'docker://quay.io/biocontainers/mulled-v2-ad317f19f5881324e963f6a6d464d696a2825ab6:c59b7a73c87a9fe81737d5d628e10a3b5807f453-0',
'cutadapt': 'docker://quay.io/biocontainers/cutadapt:2.9--py37h516909a_0',
'debian': 'docker://debian:buster-slim',
'fastqc': 'docker://quay.io/biocontainers/fastqc:0.11.7--4',
......
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