all vcf file

tasks/filtered_benchmark.wdl

@@ -8,21 +8,43 @@ task filtered_benchmark {
 	String disk_size
 	
 	command <<<
-		# get filtered chr and pos
 		cat ${chromo_consensus} | cut -f1-7 | grep notConsensus > ${chromo}.filtered.txt
 		cat ${chromo_consensus} | cut -f1-7 | grep '\./\.' >> ${chromo}.filtered.txt
-		# get benchmark chr and pos
 		zcat ${LCL5_benchmark_call} | grep -v '##' | grep -w ${chromo} > LCL5.benchmark.${chromo}.txt
-		# get vcf infomation
-		cat ${LCL5_info_dir}/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518_mendelian_vcfInfo.vcf | grep -v '##' > Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518_mendelian_vcfInfo.txt
-		python /opt/get_filtered_benchmark_vcfinfo.py -filtered ${chromo}.filtered.txt -benchmark LCL5.benchmark.${chromo}.txt -vcf Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518_mendelian_vcfInfo.txt -filename Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518.${chromo}
+		
+		echo '''Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518_mendelian_vcfInfo.vcf       Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518
+Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530_mendelian_vcfInfo.vcf       Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530
+Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530_mendelian_vcfInfo.vcf       Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530
+Quartet_DNA_BGI_T7_WGE_LCL5_1_20191105_mendelian_vcfInfo.vcf    Quartet_DNA_BGI_T7_WGE_LCL5_1_20191105
+Quartet_DNA_BGI_T7_WGE_LCL5_2_20191105_mendelian_vcfInfo.vcf    Quartet_DNA_BGI_T7_WGE_LCL5_2_20191105
+Quartet_DNA_BGI_T7_WGE_LCL5_3_20191105_mendelian_vcfInfo.vcf    Quartet_DNA_BGI_T7_WGE_LCL5_3_20191105
+Quartet_DNA_ILM_Nova_ARD_LCL5_1_20181108_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_Nova_ARD_LCL5_1_20181108
+Quartet_DNA_ILM_Nova_ARD_LCL5_2_20181108_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_Nova_ARD_LCL5_2_20181108
+Quartet_DNA_ILM_Nova_ARD_LCL5_3_20181108_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_Nova_ARD_LCL5_3_20181108
+Quartet_DNA_ILM_Nova_ARD_LCL5_4_20190111_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_Nova_ARD_LCL5_4_20190111
+Quartet_DNA_ILM_Nova_ARD_LCL5_5_20190111_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_Nova_ARD_LCL5_5_20190111
+Quartet_DNA_ILM_Nova_ARD_LCL5_6_20190111_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_Nova_ARD_LCL5_6_20190111
+Quartet_DNA_ILM_Nova_BRG_LCL5_1_20180930_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_Nova_BRG_LCL5_1_20180930
+Quartet_DNA_ILM_Nova_BRG_LCL5_2_20180930_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_Nova_BRG_LCL5_2_20180930
+Quartet_DNA_ILM_Nova_BRG_LCL5_3_20180930_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_Nova_BRG_LCL5_3_20180930
+Quartet_DNA_ILM_Nova_WUX_LCL5_1_20190917_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_Nova_WUX_LCL5_1_20190917
+Quartet_DNA_ILM_Nova_WUX_LCL5_2_20190917_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_Nova_WUX_LCL5_2_20190917
+Quartet_DNA_ILM_Nova_WUX_LCL5_3_20190917_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_Nova_WUX_LCL5_3_20190917
+Quartet_DNA_ILM_XTen_ARD_LCL5_1_20170403_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_XTen_ARD_LCL5_1_20170403
+Quartet_DNA_ILM_XTen_ARD_LCL5_2_20170403_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_XTen_ARD_LCL5_2_20170403
+Quartet_DNA_ILM_XTen_ARD_LCL5_3_20170403_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_XTen_ARD_LCL5_3_20170403
+Quartet_DNA_ILM_XTen_NVG_LCL5_1_20170329_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_XTen_NVG_LCL5_1_20170329
+Quartet_DNA_ILM_XTen_NVG_LCL5_2_20170329_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_XTen_NVG_LCL5_2_20170329
+Quartet_DNA_ILM_XTen_NVG_LCL5_3_20170329_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_XTen_NVG_LCL5_3_20170329
+Quartet_DNA_ILM_XTen_WUX_LCL5_1_20170216_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_XTen_WUX_LCL5_1_20170216
+Quartet_DNA_ILM_XTen_WUX_LCL5_2_20170216_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_XTen_WUX_LCL5_2_20170216
+Quartet_DNA_ILM_XTen_WUX_LCL5_3_20170216_mendelian_vcfInfo.vcf  Quartet_DNA_ILM_XTen_WUX_LCL5_3_20170216''' > LCL5_vcf_files
 
-		cat ${LCL5_info_dir}/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530_mendelian_vcfInfo.vcf | grep -v '##' > Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530_mendelian_vcfInfo.txt
-		python /opt/get_filtered_benchmark_vcfinfo.py -filtered ${chromo}.filtered.txt -benchmark LCL5.benchmark.${chromo}.txt -vcf Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530_mendelian_vcfInfo.txt -filename Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530.${chromo}
-
-		cat ${LCL5_info_dir}/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530_mendelian_vcfInfo.vcf | grep -v '##' > 
-		Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530_mendelian_vcfInfo.txt
-		python /opt/get_filtered_benchmark_vcfinfo.py -filtered ${chromo}.filtered.txt -benchmark LCL5.benchmark.${chromo}.txt -vcf Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530_mendelian_vcfInfo.txt -filename Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530.${chromo}
+		cat LCL5_vcf_files | while read a b
+		do
+			cat ${LCL5_info_dir}/$a | grep -v '##' > $b.txt
+			python /opt/get_filtered_benchmark_vcfinfo.py -filtered ${chromo}.filtered.txt -benchmark LCL5.benchmark.${chromo}.txt -vcf $b.txt -filename $b.${chromo}
+		done
 
 	>>>