Commit eb70cc38 authored by van den Berg's avatar van den Berg
Browse files

Update mulled container

This way, the same version of picard is used in all tasks in the
pipeline. This fixes issue #38
parent 09661984
Pipeline #3967 passed with stages
in 36 minutes and 20 seconds
......@@ -73,7 +73,7 @@ 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",
"bwa-0.7.17-picard-2.18.7": "docker://quay.io/biocontainers/mulled-v2-002f51ea92721407ef440b921fb5940f424be842:43ec6124f9f4f875515f9548733b8b4e5fed9aa6-0",
"bwa-0.7.17-picard-2.22.8": "docker://quay.io/biocontainers/mulled-v2-002f51ea92721407ef440b921fb5940f424be842:76d16eabff506ac13338d7f14644a0ad301b9d7e-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",
......@@ -174,7 +174,7 @@ rule align:
params:
rg = "@RG\\tID:{sample}-library-{read_group}\\tSM:{sample}\\tLB:library\\tPL:ILLUMINA"
output: "{sample}/bams/{sample}-{read_group}.sorted.bam"
container: containers["bwa-0.7.17-picard-2.18.7"]
container: containers["bwa-0.7.17-picard-2.22.8"]
shell: "bwa mem -t 8 -R '{params.rg}' {input.ref} {input.r1} {input.r2} "
"| picard -Xmx4G -Djava.io.tmpdir={input.tmp} SortSam "
"CREATE_INDEX=TRUE TMP_DIR={input.tmp} "
......
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