Add bamstats

biopet/bamstats.wdl

+version 1.0
+
+# Copyright Sequencing Analysis Support Core - Leiden University Medical Center 2018
+
+task Generate {
+    input {
+        String? preCommand
+        File? toolJar
+        File bam
+        File bamIndex
+        File? bedFile
+        Boolean scatterMode = false
+        Boolean onlyUnmapped = false
+        Boolean tsvOutputs = false
+        String outputDir
+        File? reference
+        File? referenceDict
+        Int memory = 4
+        Float memoryMultiplier = 2.0
+    }
+
+    String toolCommand = if defined(toolJar)
+        then "java -Xmx" + memory + "G -jar " + toolJar
+        else "biopet-bamstats -Xmx" + memory + "G"
+
+    command {
+        set -e -o pipefail
+        ~{preCommand}
+        mkdir -p ~{outputDir}
+        ~{toolCommand} Generate \
+        --bam ~{bam} \
+        ~{"--bedFile " + bedFile} \
+        ~{"--reference " + reference} \
+        ~{true="--onlyUnmapped" false="" onlyUnmapped} \
+        ~{true="--scatterMode" false="" scatterMode} \
+        ~{true="--tsvOutputs" false="" tsvOutputs} \
+        --outputDir ~{outputDir}
+    }
+
+    output {
+        File json = outputDir + "/bamstats.json"
+        File summaryJson = outputDir + "/bamstats.summary.json"
+    }
+
+    runtime {
+        memory: ceil(memory * memoryMultiplier)
+    }
+}
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