mixcr

tasks/mixcr.wdl

@@ -28,6 +28,13 @@ task mixcr {
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File sam = base + ".vdjca"
+		File align_out = base + ".vdjca"
+		File assemble_rescued_1_out = base + "_rescued_1.vdjca"
+		File assemble_rescued_2_out = base + "_rescued_2.vdjca"
+		File assemble_rescued_extended_out = base + "_rescued_2_extended.vdjca"
+		File clns_out = base + ".clns"
+		File clones_out = base + ".txt"
+		File trb_out = base + ".TRB.txt"
+		File igh_out = base + ".IGH.txt"
 	}
 }