add varDict

vardict.wdl

+version 1.0
+
+task VarDict {
+    input {
+        String? installDir
+
+        File tumorBam
+        File normalBam
+        File refFasta
+        File bedFile
+        String tumorSampleName
+        String normalSampleName
+        String outputVcf
+
+        Int chromosomeColumn = 1
+        Int startColumn = 2
+        Int endColumn = 3
+        Int geneColumn = 4
+
+        String? preCommand
+    }
+
+    String toolCommand = if defined(installDir)
+        then installDir + "/VarDict"
+        else "vardict"
+
+    command {
+        set -e -o pipefail
+        ~{preCommand}
+        ~{toolCommand} \
+        -G ~{refFasta} \
+        -N ~{tumorSampleName} \
+        -b "~{tumorBam}|~{normalBam}" \
+        -c ~{chromosomeColumn} \
+        -S ~{startColumn} \
+        -E ~{endColumn} \
+        -g ~{geneColumn} \
+        ~{bedFile} | \
+        ~{installDir + "/"}testsomatic.R | \
+        ~{installDir + "/"}var2vcf_paired.pl \
+        -N "~{tumorSampleName}|~{normalSampleName}" \
+        > ~{outputVcf}
+    }
+
+    output {
+        File vcfFile = outputVcf
+    }
+}
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