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:
rg = "@RG\\tID:{sample}_lib1\\tSM:{sample}\\tPL:ILLUMINA"
output: temp("{sample}/bams/{sample}.sorted.bam")
singularity: "docker://"
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 "
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment