first commit

inputs

@@ -13,7 +13,9 @@
   "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}",
   "{{ project_name }}.database": "{{ database }}",
   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
-  "{{ project_name }}.inputponfile": "oss://share-data-temp/TNBC/vcf",
+  "{{ project_name }}.pon_vcf1": "oss://share-data-temp/TNBC/vcf/FUSCCTNBC083_pon.vcf",
+  "{{ project_name }}.pon_vcf2": "oss://share-data-temp/TNBC/vcf/FUSCCTNBC330_pon.vcf",
+  "{{ project_name }}.pon_vcf3": "oss://share-data-temp/TNBC/vcf/FUSCCTNBC467_pon.vcf",
   "{{ project_name }}.regions": "{{ regions }}",
   "{{ project_name }}.PONmode": "{{ PONmode }}",
   "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}",

tasks/bcftools.wdl

@@ -1,6 +1,8 @@
 task bcftools {
 
-	String pon_vcf
+	File pon_vcf1
+	File pon_vcf2
+	File pon_vcf3
 	String docker
 	String cluster_config
 	String disk_size
@@ -15,11 +17,18 @@ task bcftools {
 			mkdir -p /cromwell_root/tmp/bcftools/
 			#for i in ${sep=" " pon_vcf}
 			#do
-			for i in ${pon_vcf}/*
-			do 
-				cp $i /cromwell_root/tmp/bcftools/
-				bcftools view /cromwell_root/tmp/bcftools/$i -Oz -o /cromwell_root/tmp/bcftools/$i.gz
-			done
+			#for i in ${pon_vcf}/*
+			#do 
+			#	cp $i /cromwell_root/tmp/bcftools/
+			#	bcftools view /cromwell_root/tmp/bcftools/$i -Oz -o /cromwell_root/tmp/bcftools/$i.gz
+			#done
+			
+			cp ${pon_vcf1} /cromwell_root/tmp/bcftools/
+			bcftools view /cromwell_root/tmp/bcftools/${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf1}.gz
+			cp ${pon_vcf2} /cromwell_root/tmp/bcftools/
+			bcftools view /cromwell_root/tmp/bcftools/${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf2}.gz
+			cp ${pon_vcf3} /cromwell_root/tmp/bcftools/
+			bcftools view /cromwell_root/tmp/bcftools/${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf3}.gz
 			
 			bcftools merge -m any -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ 
 			bcftools plugin fill-AN-AC |\ 

workflow.wdl

@@ -39,13 +39,17 @@ workflow {{ project_name }} {
 	Boolean set_vcf2maf
 
 
-	String inputponfile
+	File pon_vcf1
+	File pon_vcf2
+	File pon_vcf3
 	#Array[Array[File]] bcf = read_tsv(inputponfile)
 
 	call bcftools.bcftools as bcftools {
 		input:
 		PONmode=PONmode,
-		pon_vcf=inputponfile,
+		pon_vcf1=pon_vcf1,
+		pon_vcf2=pon_vcf2,
+		pon_vcf3=pon_vcf3,
 		docker=bcftools_docker,
 		disk_size=disk_size,
 		cluster_config=cluster_config