Commit a61c0c64 authored by Sander Bollen's avatar Sander Bollen
Browse files

set tmpdir for align step

parent 205f1106
Pipeline #2634 failed with stages
in 1 minute and 53 seconds
......@@ -288,14 +288,15 @@ rule align:
input:
r1 = "{sample}/pre_process/{sample}.cutadapt_R1.fastq",
r2 = "{sample}/pre_process/{sample}.cutadapt_R2.fastq",
ref = REFERENCE
ref = REFERENCE,
temp = ancient("tmp")
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 "
"| picard SortSam CREATE_INDEX=TRUE TMP_DIR={input.temp} "
"INPUT=/dev/stdin OUTPUT={output} SORT_ORDER=coordinate"
rule markdup:
......
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