Commit 2e5bee02 authored by Sander Bollen's avatar Sander Bollen
Browse files

add multicontainer for align rule

parent 5409bd9e
Pipeline #2560 passed with stages
in 18 minutes and 24 seconds
......@@ -290,6 +290,7 @@ rule align:
params:
rg = "@RG\\tID:{sample}_lib1\\tSM:{sample}\\tPL:ILLUMINA"
output: temp("{sample}/bams/{sample}.sorted.bam")
singularity: "docker://quay.io/biocontainers/mulled-v2-002f51ea92721407ef440b921fb5940f424be842:43ec6124f9f4f875515f9548733b8b4e5fed9aa6-0"
conda: "envs/bwa.yml"
shell: "bwa mem -t 8 -R '{params.rg}' {input.ref} {input.r1} {input.r2} "
"| picard SortSam CREATE_INDEX=TRUE TMP_DIR=null "
......
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