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Commit 1a455271 authored by Cats's avatar Cats
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memory Int -> String part 2

parent abd99d15
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......@@ -28,15 +28,14 @@ task VarDict {
Float minimumAlleleFrequency = 0.02
Int threads = 1
Int memory = 16
Float memoryMultiplier = 2.5
String memory = "40G"
String javaXmx = "16G"
String dockerImage = "quay.io/biocontainers/vardict-java:1.5.8--1"
}
command {
set -e -o pipefail
export JAVA_OPTS="-Xmx~{memory}G"
export JAVA_OPTS="-Xmx~{javaXmx}"
vardict-java \
~{"-th " + threads} \
-G ~{referenceFasta} \
......@@ -67,7 +66,7 @@ task VarDict {
runtime {
cpu: threads + 2
memory: ceil(memory * memoryMultiplier)
memory: memory
docker: dockerImage
}
}
......@@ -117,9 +117,11 @@ task Newref {
File bedFile = outputBed
}
Int memory = 2 + ceil(length(inputBeds) * 0.15)
runtime {
docker: dockerImage
memory: 2 + ceil(length(inputBeds) * 0.15)
memory: "~{memory}G"
}
}
......
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