first commit

tasks/mendelian.wdl

@@ -29,7 +29,7 @@ task mendelian {
 		mkdir VBT_D5_outside
 		/opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_vcf_outside} -father ${family_vcf_outside} -child ${family_vcf_outside} -pedigree ${family_name}.D5.ped -outDir VBT_D5_outside -out-prefix ${family_name}.D5.outside --output-violation-regions -thread-count $nt
 
-		cat VBT_D5_inside/${family_name}.D5.outside_trio.vcf > ${family_name}.D5.outside.vcf
+		cat VBT_D5_outside/${family_name}.D5.outside_trio.vcf > ${family_name}.D5.outside.vcf
 
 
 		echo -e "${family_name}\tLCL8\t0\t0\t2\t-9\n${family_name}\tLCL7\t0\t0\t1\t-9\n${family_name}\tLCL6\tLCL7\tLCL8\t2\t-9" > ${family_name}.D6.ped
@@ -48,7 +48,7 @@ task mendelian {
 		mkdir VBT_D6_outside
 		/opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_vcf_outside} -father ${family_vcf_outside} -child ${family_vcf_outside} -pedigree ${family_name}.D6.ped -outDir VBT_D6_outside -out-prefix ${family_name}.D6.outside --output-violation-regions -thread-count $nt
 
-		cat VBT_D6_inside/${family_name}.D6.outside_trio.vcf > ${family_name}.D6.outside.vcf
+		cat VBT_D6_outside/${family_name}.D6.outside_trio.vcf > ${family_name}.D6.outside.vcf
 	>>>
 
 	runtime {