add tcr

tasks/mixcr.wdl

@@ -16,10 +16,12 @@ task mixcr {
 		mixcr extend ${base}_rescued_2.vdjca ${base}_rescued_2_extended.vdjca
 		mixcr assemble ${base}_rescued_2_extended.vdjca ${base}.clns
 		mixcr exportClones ${base}.clns ${base}.txt
+		mixcr exportClones -c TCR ${base}.clns ${base}.TCR.txt
 		mixcr exportClones -c TRB ${base}.clns ${base}.TRB.txt
 		mixcr exportClones -c TRA ${base}.clns ${base}.TRA.txt
 		mixcr exportClones -c TRD ${base}.clns ${base}.TRD.txt
 		mixcr exportClones -c TRG ${base}.clns ${base}.TRG.txt
+		mixcr exportClones -c IG ${base}.clns ${base}.BCR.txt
 		mixcr exportClones -c IGH ${base}.clns ${base}.IGH.txt
 
 	>>>
@@ -37,10 +39,12 @@ task mixcr {
 		File assemble_rescued_extended_out = base + "_rescued_2_extended.vdjca"
 		File clns_out = base + ".clns"
 		File clones_out = base + ".txt"
+		File trb_out = base + ".TCR.txt"
 		File trb_out = base + ".TRB.txt"
 		File tra_out = base + ".TRA.txt"
 		File trd_out = base + ".TRD.txt"
 		File trg_out = base + ".TRG.txt"
+		File igh_out = base + ".BCR.txt"
 		File igh_out = base + ".IGH.txt"
 	}
 }