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Commit 5939f705 authored by Cats's avatar Cats
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Revert "add FixMateInformation"

This reverts commit ce2679ec.
parent ce2679ec
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1 merge request!70Some new tasks and memory setting changes
......@@ -199,47 +199,6 @@ task CollectTargetedPcrMetrics {
}
}
task FixMateInformation {
input {
Array[File]+ inputBams
Array[File]+ inputBamsIndex
String outputBamPath
String? preCommand
String? picardJar
Int memory = 4
Float memoryMultiplier = 3.0
}
String toolCommand = if defined(picardJar)
then "java -Xmx" + memory + "G -jar " + picardJar
else "picard -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
FixMateInformation \
INPUT=~{sep=' INPUT=' inputBams} \
OUTPUT=~{outputBamPath} \
CREATE_INDEX=true \
CREATE_MD5_FILE=true
}
output {
IndexedBamFile outputBam = object {
file: outputBamPath,
index: sub(outputBamPath, ".bam$", ".bai"),
md5: outputBamPath + ".md5"
}
}
runtime {
memory: ceil(memory * memoryMultiplier)
}
}
# Combine multiple recalibrated BAM files from scattered ApplyRecalibration runs
task GatherBamFiles {
input {
......
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