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

mwalker174 · web-flow · commit 596bc9c69333 · 2019-08-06T16:36:41.000-04:00
* Enable GC correction by default in somatic and germline cnv panel workflows
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,

Original file line number	Diff line number	Diff line change
`@@ -171,7 +171,7 @@ workflow CNVGermlineCohortWorkflow {`
`171`	`171`	`preemptible_attempts = preemptible_attempts`
`172`	`172`	`}`
`173`	`173`
`174`		`- if (select_first([do_explicit_gc_correction, false])) {`
	`174`	`+ if (select_first([do_explicit_gc_correction, true])) {`
`175`	`175`	`call CNVTasks.AnnotateIntervals {`
`176`	`176`	`input:`
`177`	`177`	`intervals = PreprocessIntervals.preprocessed_intervals,`
Original file line number	Diff line number	Diff line change
`@@ -105,7 +105,7 @@ workflow CNVSomaticPanelWorkflow {`
`105`	`105`	`preemptible_attempts = preemptible_attempts`
`106`	`106`	`}`
`107`	`107`
`108`		`- if (select_first([do_explicit_gc_correction, false])) {`
	`108`	`+ if (select_first([do_explicit_gc_correction, true])) {`
`109`	`109`	`call CNVTasks.AnnotateIntervals {`
`110`	`110`	`input:`
`111`	`111`	`intervals = PreprocessIntervals.preprocessed_intervals,`