rtg in vcfstat

tasks/multiqc.wdl

@@ -28,7 +28,7 @@ task multiqc {
 		cp ${sep=" " summary} /cromwell_root/tmp/benchmark
 		for i in `ls /cromwell_root/tmp/bamqc`
 		do
-		  tar -zxvf $i
+		  tar -zxvf $i -C /cromwell_root/tmp/bamqc
 		done
 
 		multiqc /cromwell_root/tmp/

tasks/vcfstat.wdl

@@ -1,5 +1,6 @@
 task vcfstat {
-	File vcf
+	File rtg_vcf
+	File rtg_vcf_index
 	String docker
 	String cluster_config
 	String disk_size
@@ -7,7 +8,8 @@ task vcfstat {
 	command <<<
 		set -o pipefail
 		set -e
-		rtg vcfstats ${vcf} > onestats.txt
+
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfstats ${rtg_vcf} > onestats.txt
 	>>>
 
 	runtime {

workflow.wdl

@@ -49,7 +49,8 @@ workflow {{ project_name }} {
 
 		call vcfstat.vcfstat as vcfstat {
 			input:
-			vcf=sample[4]
+			rtg_vcf=benchmark.rtg_vcf
+			rtg_vcf_index=benchmark.rtg_vcf_index
 		}