添加 'workflow.wdl'

workflow.wdl

@@ -0,0 +1,50 @@
+import "./tasks/manta.wdl" as manta_calling
+import "./tasks/AnnotSV.wdl" as AnnotSV
+
+
+workflow {{ project_name }} {
+    File tumor_bam
+    File tumor_bam_bai
+    File normal_bam
+    File normal_bam_bai
+    String ref_fasta
+    File ref_dir
+    String sample_id
+    File annotsv_database
+    
+    # excute env
+    String docker_manta
+    String cluster_config
+    String disk_size
+    String docker_annotsv
+
+	call manta_calling.manta_calling as manta_calling{
+		input:
+			tumor_bam = tumor_bam,
+			tumor_bam_bai = tumor_bam_bai,
+			normal_bam = normal_bam,
+			normal_bam_bai = normal_bam_bai,
+			ref_fasta = ref_fasta,
+			ref_dir = ref_fasta_dir,
+			sample_id = sample_id,
+			docker = docker_manta,
+			cluster_config = cluster_config,
+			disk_size = disk_size
+
+	}
+
+	call AnnotSV.AnnotSV as delly_AnnotSV{
+		input:
+                sample=sample_id,
+                somatic_vcf= manta_calling.manta_indel_vcf,
+                annotsv_database=annotsv_database,
+                docker=docker_annotsv,
+                cluster_config=cluster_config,
+                disk_size=disk_size
+		
+	}
+
+
+
+
+}