Alter: workflow

samples.json

@@ -1,9 +1,9 @@
 {
-	"vcf": [
-    ["oss://choppy-cromwell-result/test-choppy/..._pon.vcf",]
-    ["oss://choppy-cromwell-result/test-choppy/..._pon.vcf",]
-    ["oss://choppy-cromwell-result/test-choppy/..._pon.vcf",]
+    "normal_recaled_bam_bai": [
+    ["CBCGA372775_tumor", "oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA372775_tumor.sorted.deduped.bam","oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA372775_tumor.sorted.deduped.bam.bai"],
+    ["CBCGA380400_tumor","oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA380400_tumor.sorted.deduped.bam","oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA380400_tumor.sorted.deduped.bam.bai"],
+    ["CBCGA382368_tumor","oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA382368_tumor.sorted.deduped.bam","oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA382368_tumor.sorted.deduped.bam.bai"]
     ],
-	"panel_id": "PON_20210407",
-	"sample_id": "PON_20210407"
+    "panel_id": "PON_20210407_test",
+    "sample_id": "PON_20210407_test"
 }

workflow.wdl

@@ -14,7 +14,7 @@ workflow {{ project_name }} {
 	String dbsnp
 	File regions
 
-	Array[Array[File]] normal_recaled_bam_bai
+	Array[File] normal_recaled_bam_bai
 	String sentieon_docker
 	String cluster_config
 	String disk_size