更新 'workflow.wdl'

workflow.wdl

@@ -1,23 +1,27 @@
-import "./tasks/BAMReadCount.wdl" as BAMReadCount
+task BAMReadCount {
 
-workflow {{ project_name }} {
-	File reference
-	File bedfile
-	File bamfile
 	String sample_id
+	File fa
+	File fai
+	File bed
+	File bam
+	File bai
 	String docker
 	String cluster_config
 	String disk_size
-	
 
-	call BAMReadCount.BAMReadCount as BAMReadCount {
-		input:
-		reference = reference,
-		bedfile = bedfile,
-		bamfile = bamfile,
-		docker = docker,
-		disk_size = disk_size,
-		cluster_config=cluster_config,
-		sample_id=sample_id
+	command <<<
+		bam-readcount -f ${reference} -l ${bedfile} ${bamfile} > ${sample_id}.readcount
+	>>>
+
+	runtime {
+		docker: docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File BAMReadCount = "${sample_id}.readcount"
 	}
 }