mixcr

tasks/align.wdl → tasks/mixcr.wdl

@@ -1,4 +1,4 @@
-task align {
+task mixcr {
 
 	File read1
 	File read2
@@ -11,6 +11,14 @@ task align {
 
 	command <<<
         mixcr align -p rna-seq -s hsa -OallowPartialAlignments=true ${read1} ${read2} ${base}.vdjca
+		mixcr assemblePartial ${base}.vdjca ${base}_rescued_1.vdjca
+		mixcr assemblePartial ${base}_rescued_1.vdjca ${base}_rescued_2.vdjca
+		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 TRB ${base}.clns ${base}.TRB.txt
+		mixcr exportClones -c IGH ${base}.clns ${base}.IGH.txt
+
 	>>>
 
 	runtime {

workflow.wdl

@@ -1,4 +1,4 @@
-import "./tasks/align.wdl" as align
+import "./tasks/mixcr.wdl" as mixcr
 
 workflow {{ project_name }} {
 
@@ -10,7 +10,7 @@ workflow {{ project_name }} {
   	String disk_size
 	
 	
-	call align.align as align {
+	call mixcr.mixcr as mixcr {
 		input: 
 		read1=read1, 
 		read2=read2,