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Commit 3cb3a224 authored by Ruben Vorderman's avatar Ruben Vorderman
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fix bwamem task

parent e10f8acc
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1 merge request!11Changes needed for the iterative assembly pipeline
task BwaMem {
task mem {
String? preCommand
File inputR1
File? inputR2
......@@ -10,6 +10,7 @@ task BwaMem {
Int? threads
Int? memory
command {
set -e -o pipefail
mkdir -p $(dirname ${outputPath})
......@@ -23,8 +24,8 @@ task BwaMem {
File bamFile = outputPath
}
runtime{
cpu: if defined(threads) then threads else 1
memory: if defined(memory) then memory else 8
cpu: select_first([threads,1])
memory: select_first([memory,8])
}
}
......
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