added bwa mem

bwa.wdl

+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])
+        }
+}
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