task dbsnp location

tasks/VQSR.wdl

@@ -19,13 +19,13 @@ command <<<
 		set -e
 		export SENTIEON_LICENSE=192.168.0.55:8990
 
-		resource_text="--resource ${dbsnp_1000G_phase1} \
+		resource_text="--resource ${ref_dir}/${dbsnp_1000G_phase1} \
               --resource_param 1000G,known=false,training=true,truth=false,prior=10.0 "
-		resource_text="$resource_text --resource ${dbsnp_1000G_omni} \
+		resource_text="$resource_text --resource ${ref_dir}/${dbsnp_1000G_omni} \
               --resource_param omni,known=false,training=true,truth=true,prior=12.0 "
-		resource_text="$resource_text --resource ${dbsnp} \
+		resource_text="$resource_text --resource ${ref_dir}/${dbsnp} \
               --resource_param dbsnp,known=true,training=false,truth=false,prior=2.0 "
-		resource_text="$resource_text --resource ${dbsnp_hapmap} \
+		resource_text="$resource_text --resource ${ref_dir}/${dbsnp_hapmap} \
               --resource_param hapmap,known=false,training=true,truth=true,prior=15.0"
 
         annotation_array="DP QD FS SOR MQ MQRankSum ReadPosRankSum"
@@ -37,9 +37,9 @@ command <<<
   		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo ApplyVarCal -v ${vcf} --var_type SNP --tranches_file ${sample}.vqsrSNP.hc.tranches --sensitivity 99.0 --recal ${sample}.vqsrSNP.hc.recal ${sample}.vqsrSNP.hc.recaled.vcf.gz
   		${SENTIEON_INSTALL_DIR}/bin/sentieon plot vqsr -o ${sample}.vqsrSNP.pdf ${sample}.vqsrSNP.hc.plotfile
 
-  		resource_text="$resource_text --resource ${dbsnp_Mill} \
+  		resource_text="$resource_text --resource ${ref_dir}/${dbsnp_Mill} \
               --resource_param Mills,known=false,training=true,truth=true,prior=12.0 "
-		resource_text="$resource_text --resource ${dbsnp} \
+		resource_text="$resource_text --resource ${ref_dir}/${dbsnp} \
               --resource_param dbsnp,known=true,training=false,truth=false,prior=2.0 "
 
         annotation_array="QD DP FS SOR MQ ReadPosRankSum"