Added markdup step

samtools.wdl

@@ -21,4 +21,30 @@ task Merge {
     output {
         File outputBam = outputBamPath
     }
-}
\ No newline at end of file
+}
+
+task Markdup {
+    File inputBam
+    String outputBamPath
+
+    command {
+        samtools markdup ${inputBam} ${outputBamPath}
+    }
+
+    output {
+        File outputBam = outputBamPath
+    }
+}
+
+task Flagstat {
+    File inputBam
+    String outputPath
+
+    command {
+        samtools flagstat ${inputBam} > ${outputPath}
+    }
+
+    output {
+        File flagstat = outputPath
+    }
+}