Enable gc correction by default in cnv workflows (#5966)

* Enable GC correction by default in somatic and germline cnv panel workflows
broadinstitute · Aug 6, 2019 · 596bc9c · 596bc9c
1 parent 06df7e8
commit 596bc9c
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
@@ -171,7 +171,7 @@ workflow CNVGermlineCohortWorkflow {
             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,

diff --git a/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl b/scripts/cnv_wdl/somatic/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,