Merge pull request #43 from broadinstitute/cnv_benchmark_yg

Wittyer WDL Output Updates
broadinstitute · Sep 8, 2023 · 2b623f4 · 2b623f4
2 parents e5c0d27 + f60b350
commit 2b623f4
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/BenchmarkCNV/BenchmarkCNV/BenchmarkCNV.wdl b/BenchmarkCNV/BenchmarkCNV/BenchmarkCNV.wdl
@@ -83,6 +83,10 @@ workflow Benchmark_CNV_Caller {
             ~{'--includeBed '+ bedfile} \
             -o ~{truth_sample_name}_wittyer_output
 
+            # Move wittyer output to the output directory
+            mv ~{truth_sample_name}_wittyer_output/Wittyer.*.Vs.*.vcf.gz ~{truth_sample_name}_wittyer_output/Wittyer.~{truth_sample_name}.Vs.~{query_sample_name}.vcf.gz
+            mv ~{truth_sample_name}_wittyer_output/Wittyer.*.Vs.*.vcf.gz.tbi ~{truth_sample_name}_wittyer_output/Wittyer.~{truth_sample_name}.Vs.~{query_sample_name}.vcf.gz.tbi
+
         >>>
         runtime {
             docker: wittyer_docker