ped file

tasks/mendelian.wdl

@@ -10,22 +10,22 @@ task mendelian {
 	command <<<
 		export LD_LIBRARY_PATH=/opt/htslib-1.9
 		nt=$(nproc)
-	# prepare ped file, D5
-		echo "${chromo}	LCL8_consensus_calls	0	0	2	-9
-		${chromo}	LCL7_consensus_calls	0	0	1	-9
-		${chromo}	LCL5_consensus_calls	LCL7_consensus_calls	LCL8_consensus_calls	2	-9" > ${chromo}.D5.ped
+
+		echo "${chromo}	LCL8_consensus_call	0	0	2	-9
+		${chromo}	LCL7_consensus_call	0	0	1	-9
+		${chromo}	LCL5_consensus_call	LCL7_consensus_call	LCL8_consensus_call	2	-9" > ${chromo}.D5.ped
 
 		mkdir VBT_D5
 		/opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${consensus_vcf} -father ${consensus_vcf} -child ${consensus_vcf} -pedigree ${chromo}.D5.ped -outDir VBT_D5 -out-prefix ${chromo}.D5 --output-violation-regions -thread-count $nt
 
 		cat VBT_D5/${chromo}.D5_trio.vcf > ${chromo}.D5.vcf
-	# prepare ped file, D6
-		echo "${chromo}	LCL8_consensus_calls	0	0	2	-9
-		${chromo}	LCL7_consensus_calls	0	0	1	-9
-		${chromo}	LCL6_consensus_calls	LCL7_consensus_calls	LCL8_consensus_calls	2	-9" > ${chromo}.D6.ped
+
+		echo "${chromo}	LCL8_consensus_call	0	0	2	-9
+		${chromo}	LCL7_consensus_call	0	0	1	-9
+		${chromo}	LCL6_consensus_call	LCL7_consensus_call	LCL8_consensus_call	2	-9" > ${chromo}.D6.ped
 
 		mkdir VBT_D6
-		/opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${consensus_vcf} -father ${consensus_vcf} -child ${consensus_vcf} -pedigree ${chromo}.D5.ped -outDir VBT_D6 -out-prefix ${chromo}.D6 --output-violation-regions -thread-count $nt
+		/opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${consensus_vcf} -father ${consensus_vcf} -child ${consensus_vcf} -pedigree ${chromo}.D6.ped -outDir VBT_D6 -out-prefix ${chromo}.D6 --output-violation-regions -thread-count $nt
 
 		cat VBT_D6/${chromo}.D6_trio.vcf > ${chromo}.D6.vcf
 	>>>
@@ -37,6 +37,8 @@ task mendelian {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
+		File D5_ped = "${chromo}.D5.ped"
+		File D6_ped = "${chromo}.D6.ped"
 		Array[File] D5_mendelian = glob("VBT_D5/*")
 		Array[File] D6_mendelian = glob("VBT_D6/*")
 		File D5_trio_vcf = "${chromo}.D5.vcf"