更新 'workflow.wdl'

workflow.wdl

@@ -1,4 +1,5 @@
 import "./tasks/CNVkit.wdl" as cnvkit
+import "./tasks/CNVkit_multi_REF.wdl" as cnvkit_multi
 import "./tasks/AnnotSV.wdl" as AnnotSV
 
 workflow {{ project_name }} {
@@ -14,8 +15,6 @@ workflow {{ project_name }} {
     File tumor_bam_bai
     File? normal_bam
     File? normal_bam_bai
-    #File? inputBams
-    #File? inputBamIndexs
     Array[File]? inputBams
     Array[File]? inputBamIndexs
     String docker_cnvkit
@@ -25,8 +24,9 @@ workflow {{ project_name }} {
     String docker_annotsv
     String docker_sequenza
 
-    call cnvkit.cnvkit as cnvkit{
-        input:
+	if defined(inputBams) && size(inputBams) > 0 {
+	    call cnvkit_multi.cnvkit_multi as cnvkit_multi{
+            input:
             sample_id=sample_id,
             ref_dir=ref_fasta_cnvkit,
             fasta=ref_fasta,
@@ -35,14 +35,31 @@ workflow {{ project_name }} {
             bed_file=bed_file,
             tumor_bam=tumor_bam,
             tumor_bam_index=tumor_bam_bai,
-            normal_bam=normal_bam,
-            normal_bam_index=normal_bam_bai,
             normal_bams = inputBams,
             normal_bam_indexs = inputBamIndexs,
             docker=docker_cnvkit,
             cluster_config=cluster_config,
             disk_size=disk_size
     }
+    } else {
+        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,
+                docker=docker_cnvkit,
+                cluster_config=cluster_config,
+                disk_size=disk_size
+        }
+    }
+
 
 	call AnnotSV.AnnotSV as cnvkit_AnnotSV{
 		input: