Merge pull request #26 from biowdl/macs2

Macs2

macs2.wdl

+task PeakCalling {
+    String? preCommand
+    Array[File] bamFiles
+    String outDir
+    String sampleName
+    Int? threads
+    Int? memory
+
+    command {
+        set -e -o pipefail
+        ${preCommand}
+        macs2 callpeaks \
+        --treatment ${sep = ' ' bamFiles} \
+        --outdir ${outDir} \
+        --name ${sampleName}
+    }
+
+    output {
+        File peakFile = outDir + "/" + sampleName + "/macs2/" + sampleName + "_peaks.narrowPeak"
+    }
+
+    runtime {
+        cpu: select_first([threads,1])
+        memory: select_first([memory,8])
+    }
+}
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