first commit

defaults

@@ -13,6 +13,7 @@
     "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
     "database": "oss://pgx-reference-data/annovar/",
     "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/agilent_v6.bed",
+    "BCF" : ["oss://share-data-temp/TNBC/vcf/FUSCCTNBC083_pon.vcf","oss://share-data-temp/TNBC/vcf/FUSCCTNBC330_pon.vcf","oss://share-data-temp/TNBC/vcf/FUSCCTNBC467_pon.vcf"],
     "PONmode": true,
     "cosmic_vcf": "CosmicCodingMuts.hg19.v91.vcf",
     "cosmic_dir": "oss://pgx-reference-data/reference/cosmic/",

inputs

@@ -12,7 +12,7 @@
   "{{ project_name }}.vcf2maf_r_docker": "{{ vcf2maf_r_docker }}",
   "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}",
   "{{ project_name }}.database": "{{ database }}",
-  "{{ project_name }}.bcf": ["oss://share-data-temp/TNBC/vcf/FUSCCTNBC083_pon.vcf","oss://share-data-temp/TNBC/vcf/FUSCCTNBC330_pon.vcf","oss://share-data-temp/TNBC/vcf/FUSCCTNBC467_pon.vcf"],
+  "{{ project_name }}.BCF": "{{ BCF }}",
   "{{ project_name }}.regions": "{{ regions }}",
   "{{ project_name }}.PONmode": "{{ PONmode }}",
   "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}",

workflow.wdl

@@ -38,9 +38,9 @@ workflow {{ project_name }} {
 	#File pon_vcf1
 	#File pon_vcf2
 	#File pon_vcf3
-	Array[File] bcf
+	Array[File] BCF
 
-	scatter (sample in bcf) {
+	scatter (sample in BCF) {
 		call bcftools.bcftools as bcftools {
 			input:
 			PONmode=PONmode,