rtg in vcfstat

tasks/jaccard_index.wdl

@@ -0,0 +1,29 @@
+task JI {
+	File vcf_a
+	File vcf_b
+	File dir_name
+	File sdf
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		touch number
+		cat ${filelist}| while read a b c d
+		do
+			rtg vcfeval -b $a -c $b -o $c -t ${sdf}
+			cat $c/summary.txt | sed -n '4,4p' | sed 's/\s\+/\t/g'| cut -f4-6 >> number
+		done
+		paste ${filelist} number > result.txt
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File summary = "result.txt"
+	}
+}

workflow.wdl

@@ -5,12 +5,15 @@ import "./tasks/benchmark.wdl" as benchmark
 import "./tasks/multiqc.wdl" as multiqc
 import "./tasks/vcfstat.wdl" as vcfstat
 import "./tasks/mergeNum.wdl" as mergeNum
+#import "./tasks/jaccard_index.wdl" as JI
 
 
 workflow {{ project_name }} {
 
 	File inputSamplesFile
 	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
+#	File inputJIpiarsFile
+#	Array[Array[File]] inputJIpairs = read_tsv(inputJIpiarsFile)
 	File screen_ref_dir
 	File fastq_screen_conf
 	File benchmarking_dir
@@ -49,7 +52,7 @@ workflow {{ project_name }} {
 
 		call vcfstat.vcfstat as vcfstat {
 			input:
-			rtg_vcf=benchmark.rtg_vcf
+			rtg_vcf=benchmark.rtg_vcf,
 			rtg_vcf_index=benchmark.rtg_vcf_index
 		}