test

tasks/export.wdl

@@ -10,7 +10,7 @@ task export{
 		    cp -r ${sep=" " results} /cromwell_root/tmp/cnvkit
 		    cd /cromwell_root/tmp/cnvkit
 		    # this version app just provides seg
-		    cnvkit.py export seg *.cns -o ${sample_id}.seg
+		    cnvkit.py export seg *.cns -o /cromwell_root/tmp/cnvkit/${sample_id}.seg
     >>>
    
     runtime { 
@@ -21,6 +21,6 @@ task export{
     }
 
     output {
-        File seg = "${sample_id}.seg"
+        File seg = "/cromwell_root/tmp/cnvkit/${sample_id}.seg"
     }
 }