From 4cccab3fbb25473282d7486d9a941e1292912157 Mon Sep 17 00:00:00 2001
From: meganshand <mshand@broadinstitute.org>
Date: Tue, 18 May 2021 11:55:55 -0400
Subject: [PATCH] Adding median coverage metric to mitochondria pipeline
 (#7253)

---
 scripts/mitochondria_m2_wdl/AlignAndCall.wdl         | 3 +++
 scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl | 1 +
 2 files changed, 4 insertions(+)

diff --git a/scripts/mitochondria_m2_wdl/AlignAndCall.wdl b/scripts/mitochondria_m2_wdl/AlignAndCall.wdl
index 660f03fab1f..cdec7a44589 100644
--- a/scripts/mitochondria_m2_wdl/AlignAndCall.wdl
+++ b/scripts/mitochondria_m2_wdl/AlignAndCall.wdl
@@ -263,6 +263,7 @@ workflow AlignAndCall {
     File theoretical_sensitivity_metrics = CollectWgsMetrics.theoretical_sensitivity
     File contamination_metrics = GetContamination.contamination_file
     Int mean_coverage = CollectWgsMetrics.mean_coverage
+    Float median_coverage = CollectWgsMetrics.median_coverage
     String major_haplogroup = GetContamination.major_hg
     Float contamination = FilterContamination.contamination
   }
@@ -373,6 +374,7 @@ task CollectWgsMetrics {
     R --vanilla <<CODE
       df = read.table("metrics.txt",skip=6,header=TRUE,stringsAsFactors=FALSE,sep='\t',nrows=1)
       write.table(floor(df[,"MEAN_COVERAGE"]), "mean_coverage.txt", quote=F, col.names=F, row.names=F)
+      write.table(df[,"MEDIAN_COVERAGE"], "median_coverage.txt", quote=F, col.names=F, row.names=F)
     CODE
   >>>
   runtime {
@@ -385,6 +387,7 @@ task CollectWgsMetrics {
     File metrics = "metrics.txt"
     File theoretical_sensitivity = "theoretical_sensitivity.txt"
     Int mean_coverage = read_int("mean_coverage.txt")
+    Float median_coverage = read_float("median_coverage.txt")
   }
 }
 
diff --git a/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl b/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
index 7bbadf67718..e210204a809 100644
--- a/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
+++ b/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
@@ -184,6 +184,7 @@ workflow MitochondriaPipeline {
     File contamination_metrics = AlignAndCall.contamination_metrics
     File base_level_coverage_metrics = CoverageAtEveryBase.table
     Int mean_coverage = AlignAndCall.mean_coverage
+    Float median_coverage = AlignAndCall.median_coverage
     String major_haplogroup = AlignAndCall.major_haplogroup
     Float contamination = AlignAndCall.contamination
   }