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task mem {
File read1
File referenceFile
File? read2
String? outputFile
String? preCommand
Int? threads = 1
String? memory = "4G"
Int? minimumSeedLength
Int? w
Int? d
Float? r
Int? y
Int? c
Int? D
Int? m
Int? W
Boolean? skipMateRescue
Boolean? skipPairing
Int? matchScore
Int? mismatchPenalty
String? gapOpenPenalty
String? gapExtensionPenalty
String? endClippingPenalty
String? unpairedReadPairPenalty
String? readType
Boolean? smartPairing
String? readGroupHeaderLine
String? H
Boolean? j
Boolean? five
Boolean? q
Int? K
Int? minimumOutputScore
String? h
Boolean? a
Boolean? appendComment
Boolean? V
Boolean? Y
Boolean? M
String? I
command {
set -e -o pipefail
${preCommand}
bwa mem \
${"-t " + threads } \
${"-k " + minimumSeedLength } \
${"-w " + w } \
${"-d " + d } \
${"-r " + r } \
${"-y " + y } \
${"-c " + c } \
${"-D " + D } \
${"-W " + W } \
${"-m " + m } \
${true="-s " false="" skipMateRescue } \
${true="-P " false="" skipPairing } \
${"-A " + matchScore } \
${"-B " + mismatchPenalty } \
${"-O " + gapOpenPenalty } \
${"-E " + gapExtensionPenalty } \
${"-L " + endClippingPenalty } \
${"-U " + unpairedReadPairPenalty } \
${"-x " + readType } \
${true="-p " false="" smartPairing} \
${"-r " + readGroupHeaderLine} \
${"-H " + H } \
${"-o " + outputFile } \
${true="-j" false="" j } \
${true="-5" false="" five } \
${true="-q" false="" q } \
${"-K " + K } \
${"-T " + minimumOutputScore } \
${"-h " + h } \
${true="-a" false="" a } \
${true="-C" false="" appendComment } \
${true="-V" false="" V } \
${true="-Y" false="" Y } \
${true="-M" false="" M } \
${"-I " + I } \
${referenceFile} ${read1} ${read2}
}
output {
File samFile = if defined(outputFile) then outputFile else stdout()
}
runtime {
cpu: select_first([threads])
memory: select_first([memory])
}
}