From 4a74b0855b406cc1c34615ee21d0441b0eac91b7 Mon Sep 17 00:00:00 2001
From: bshifaw <bshifaw@broadinstitute.com>
Date: Thu, 23 May 2019 17:22:05 -0400
Subject: [PATCH] Dev (#9)

* Update wdl to GATK4.1

* Updated imports to git tag URL, updated gatk docker in json, updated Readme structure

* minor edits and link to documentation in readme

* import url correction

* update to gatk4.1.1.0

* updated GATK version in Readme

* updated import url to 1.3.0

* do_explicit_gc_correction changed to be true by default
---
 cnv_somatic_panel_workflow.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cnv_somatic_panel_workflow.wdl b/cnv_somatic_panel_workflow.wdl
index f4dfcce..5c11367 100644
--- a/cnv_somatic_panel_workflow.wdl
+++ b/cnv_somatic_panel_workflow.wdl
@@ -105,7 +105,7 @@ workflow CNVSomaticPanelWorkflow {
             preemptible_attempts = preemptible_attempts
     }
 
-    if (select_first([do_explicit_gc_correction, false])) {
+    if (select_first([do_explicit_gc_correction, true])) {
         call CNVTasks.AnnotateIntervals {
             input:
                 intervals = PreprocessIntervals.preprocessed_intervals,