first commit

inputs

@@ -12,8 +12,7 @@
   "{{ project_name }}.vcf2maf_r_docker": "{{ vcf2maf_r_docker }}",
   "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}",
   "{{ project_name }}.database": "{{ database }}",
-  "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
-  "{{ 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

@@ -9,10 +9,6 @@ import "./tasks/vcf2maf.wdl" as vcf2maf
 
 workflow {{ project_name }} {
 
-	File inputSamplesFile
-	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
-	#Array[String] sample
-
 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
 	String sentieon_docker