revise-tophat

tasks/tophat2.wdl

@@ -20,7 +20,7 @@ task tophat2 {
    }
 
    output {
-      File accepted_hits = baseout + "_accepted_hits.bam"
-      File unmapped_bam = baseout + "_unmapped.bam"
+      File accepted_hits = "${baseout}/${baseout}.accepted_hits.bam"
+      File unmapped_bam = "${baseout}/${baseout}.unmapped.bam"
    }
 }