first commit

inputs

@@ -13,7 +13,7 @@
   "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}",
   "{{ project_name }}.database": "{{ database }}",
   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
-  "{{ project_name }}.inputponfile": "oss://choppy-cromwell-result/test-choppy/FUSCC_TNBC_WES_liuyaqing_20200703/67f23290-260b-4f95-abce-7206f9e4e7fa/call-PON",
+  "{{ project_name }}.inputponfile": "oss://choppy-cromwell-result/test-choppy/FUSCC_TNBC_WES_liuyaqing_20200703/vcf",
   "{{ project_name }}.regions": "{{ regions }}",
   "{{ project_name }}.PONmode": "{{ PONmode }}",
   "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}",

tasks/bcftools.wdl

@@ -13,12 +13,12 @@ task bcftools {
 		
 		if [ ${PONmode} ]; then
 			mkdir -p /cromwell_root/tmp/bcftools/
-			cp ${pon_vcf}/*.vcf /cromwell_root/tmp/bcftools/
 			#for i in ${sep=" " pon_vcf}
 			#do
-			for i in /cromwell_root/tmp/bcftools/*.vcf
+			for i in ${pon_vcf}/*
 			do 
-				bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$i.gz
+				cp $i /cromwell_root/tmp/bcftools/
+				bcftools view /cromwell_root/tmp/bcftools/$i -Oz -o /cromwell_root/tmp/bcftools/$i.gz
 			done
 			
 			bcftools merge -m any -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\