link instead of merge if one bam file

common.wdl

@@ -102,4 +102,17 @@ task appendToStringArray {
     runtime {
         memory: 1
     }
+}
+
+task createLink {
+    File inputFile
+    String outputPath
+
+    command {
+        ln -sf ${inputFile} ${outputPath}
+    }
+
+    output {
+        File link = outputPath
+    }
 }
\ No newline at end of file

samtools.wdl

@@ -21,7 +21,12 @@ task Merge {
     command {
         set -e -o pipefail
         ${preCommand}
-        samtools merge ${outputBamPath} ${sep=' ' bamFiles}
+        if [ ${length(bamFiles)} -gt 1 ]
+          then
+            samtools merge ${outputBamPath} ${sep=' ' bamFiles}
+          else
+            ln -sf ${bamFiles} ${outputBamPath}
+        fi
     }
 
     output {