更新 'workflow.wdl'

workflow.wdl

@@ -1,5 +1,6 @@
 import "./tasks/delly.wdl" as delly
 import "./tasks/AnnotSV.wdl" as AnnotSV
+import "./tasks/MSIsensor.wdl" as MSIsensor
 
 workflow {{ project_name }}{
     String sample_id
@@ -14,7 +15,9 @@ workflow {{ project_name }}{
     String cluster_config
     String disk_size
     File annotsv_database
+    File baseline
     String docker_annotsv
+    String docker_MSIsensor
 
     call delly.delly as delly{
         input:
@@ -32,10 +35,25 @@ workflow {{ project_name }}{
 
     }
 
+    call MSIsensor.MSIsensor as MSIsensor{
+        input:
+            sample = sample_id,
+            ref_dir = ref_fasta_dir,
+            fasta = ref_fasta,
+            tumor_bam=tumor_bam,
+            tumor_bam_index =tumor_bam_bai,
+            normal_bam = normal_bam,
+            normal_bam_index=normal_bam_bai,
+            baseline=baseline,
+            docker = docker_MSIsensor,
+            cluster_config = cluster_config,
+            disk_size = disk_size
+    }
+
 	call AnnotSV.AnnotSV as delly_AnnotSV{
 		input:
                 sample=sample_id,
-                somatic_vcf=cnvkit.cnv_bed,
+                somatic_vcf= delly.pass_vcf,
                 annotsv_database=annotsv_database,
                 docker=docker_annotsv,
                 cluster_config=cluster_config,