first commit

inputs

   "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}",
   "{{ project_name }}.database": "{{ database }}",
   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
-  "{{ project_name }}.inputponfile": "{{ inputponfile }}",
+  "{{ project_name }}.inputponfile": "oss://choppy-cromwell-result/test-choppy/FUSCC_TNBC_WES_liuyaqing_20200703/67f23290-260b-4f95-abce-7206f9e4e7fa/call-PON/",
   "{{ project_name }}.regions": "{{ regions }}",
   "{{ project_name }}.PONmode": "{{ PONmode }}",
   "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}",

tasks/bcftools.wdl

 task bcftools {
 
-	Array[Array[File]] pon_vcf
+	String pon_vcf
 	String docker
 	String cluster_config
 	String disk_size
 		
 		if [ ${PONmode} ]; then
 			mkdir -p /cromwell_root/tmp/bcftools/
-			for i in ${sep=" " pon_vcf}
-			do
-				bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$i.gz
-			done
+			#for i in ${sep=" " pon_vcf}
+			#do
+			bcftools view ${pon_vcf}/*.vcf -Oz -o /cromwell_root/tmp/bcftools/*.vcf.gz
+			#done
 			
 			bcftools merge -m any -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ 
 			bcftools plugin fill-AN-AC |\ 

workflow.wdl

 	Boolean set_vcf2maf
 
 
-	File inputponfile
-	Array[Array[File]] bcf = read_tsv(inputponfile)
+	String inputponfile
+	#Array[Array[File]] bcf = read_tsv(inputponfile)
 
 	call bcftools.bcftools as bcftools {
 		input:
 		PONmode=PONmode,
-		pon_vcf=bcf,
+		pon_vcf=inputponfile,
 		docker=bcftools_docker,
 		disk_size=disk_size,
 		cluster_config=cluster_config