vcf to txt

tasks/reformVCF.wdl

@@ -9,6 +9,11 @@ task reformVCF {
 
 	python /opt/reformVCF.py -vcf ${family_mendelian_info} -name ${family_name}
 
+	cat ${family_name}.LCL5.vcf | grep -v '##' | grep -v '0/0' > ${family_name}.LCL5.txt
+	cat ${family_name}.LCL6.vcf | grep -v '##' | grep -v '0/0' > ${family_name}.LCL6.txt
+	cat ${family_name}.LCL7.vcf | grep -v '##' | grep -v '0/0' > ${family_name}.LCL7.txt
+	cat ${family_name}.LCL8.vcf | grep -v '##' | grep -v '0/0' > ${family_name}.LCL8.txt
+
 	>>>
 
 	runtime {
@@ -24,6 +29,10 @@ task reformVCF {
 		File LCL7_family_info = "${family_name}.LCL7.vcf"
 		File LCL8_family_info = "${family_name}.LCL8.vcf"
 		File family_info = "${family_name}.vcf"
+		File LCL5_family_info_txt = "${family_name}.LCL5.txt"
+		File LCL6_family_info_txt = "${family_name}.LCL6.txt"
+		File LCL7_family_info_txt = "${family_name}.LCL7.txt"
+		File LCL8_family_info_txt = "${family_name}.LCL8.txt"
 	}
 }
 

tasks/variantsNorm.wdl

@@ -16,6 +16,8 @@ task variantsNorm {
 
 		/opt/hall-lab/bcftools-1.9/bin/bcftools norm -f ${ref_dir}/${fasta} ${sampleName}.filtered.vcf > ${sampleName}.normed.vcf
 
+		cat ${sampleName}.normed.vcf | grep -v '##' > ${sampleName}.normed.txt
+
 	>>>
 
 	runtime {
@@ -26,5 +28,6 @@ task variantsNorm {
 	}
 	output {
 		File normed_vcf = "${sampleName}.normed.vcf"
+		File normed_txt = "${sampleName}.normed.txt"
 	}
 }

workflow.wdl

@@ -133,32 +133,32 @@ workflow {{ project_name }} {
 		}
 		call merge_info.merge_info as LCL5mergeInfo {
 			input:
-			vcfInfo=LCL5variantsNorm.normed_vcf,
-			mendelianInfo=reformVCF.LCL5_family_info,
+			vcfInfo=LCL5variantsNorm.normed_txt,
+			mendelianInfo=reformVCF.LCL5_family_info_txt,
 			sample=quartet[4],
 			cluster_config=cluster_config,
 			disk_size=disk_size
 		}
 		call merge_info.merge_info as LCL6mergeInfo {
 			input:
-			vcfInfo=LCL6variantsNorm.normed_vcf,
-			mendelianInfo=reformVCF.LCL6_family_info,
+			vcfInfo=LCL6variantsNorm.normed_txt,
+			mendelianInfo=reformVCF.LCL6_family_info_txt,
 			sample=quartet[5],
 			cluster_config=cluster_config,
 			disk_size=disk_size
 		}
 		call merge_info.merge_info as LCL7mergeInfo {
 			input:
-			vcfInfo=LCL7variantsNorm.normed_vcf,
-			mendelianInfo=reformVCF.LCL7_family_info,
+			vcfInfo=LCL7variantsNorm.normed_txt,
+			mendelianInfo=reformVCF.LCL7_family_info_txt,
 			sample=quartet[6],
 			cluster_config=cluster_config,
 			disk_size=disk_size
 		}
 		call merge_info.merge_info as LCL8mergeInfo {
 			input:
-			vcfInfo=LCL8variantsNorm.normed_vcf,
-			mendelianInfo=reformVCF.LCL8_family_info,
+			vcfInfo=LCL8variantsNorm.normed_txt,
+			mendelianInfo=reformVCF.LCL8_family_info_txt,
 			sample=quartet[7],
 			cluster_config=cluster_config,
 			disk_size=disk_size