align

tasks/align.wdl

@@ -0,0 +1,25 @@
+task align {
+
+	File read1
+	File read2
+
+	String sample
+	String base = sub(basename(read1),"\\.\\S+$", "")
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+        mixcr align -p rna-seq -s hsa -OallowPartialAlignments=true ${read1} ${read2} ${base}.vdjca
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File sam = base + ".vdjca"
+	}
+}