添加 'workflow.wdl'

workflow.wdl

@@ -0,0 +1,58 @@
+import "./tasks/CNVkit.wdl" as cnvkit
+import "./tasks/CNVkit_multi_REF.wdl" as cnvkit_multi
+import "./tasks/AnnotSV.wdl" as AnnotSV
+
+workflow {{ project_name }} {
+    String sample_id
+    File ref_fasta_dir
+    File ref_fasta_cnvkit
+    String ref_fasta
+    File ref_flat
+    File? bed_file
+    String Ploidy
+    File gc
+    File tumor_bam
+    File tumor_bam_bai
+    File? normal_bam
+    File? normal_bam_bai
+    File? VCF
+    String docker_cnvkit
+    String cluster_config
+    String disk_size
+    File annotsv_database
+    String docker_annotsv
+    String docker_sequenza
+    call cnvkit.cnvkit as cnvkit{
+        input:
+            sample_id=sample_id,
+            ref_dir=ref_fasta_cnvkit,
+            fasta=ref_fasta,
+            ref_flat=ref_flat,
+            Ploidy=Ploidy,
+            bed_file=bed_file,
+            tumor_bam=tumor_bam,
+            tumor_bam_index=tumor_bam_bai,
+            normal_bam=normal_bam,
+            normal_bam_index=normal_bam_bai,
+            VCF = VCF,
+            docker=docker_cnvkit,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+    }
+
+    call AnnotSV.AnnotSV as cnvkit_AnnotSV{
+    input:
+        sample=sample_id,
+        somatic_vcf=cnvkit.cnv_bed,
+        annotsv_database=annotsv_database,
+        docker=docker_annotsv,
+        cluster_config=cluster_config,
+        disk_size=disk_size
+    
+}
+
+
+
+
+
+}