alter workflow parameters

defaults

@@ -20,7 +20,7 @@
     "disk_size": "200",
     "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
     "germline": "false",
-    "TNseq": "true",
-    "TNscope": "true",
-    "Varscan": "true"
+    "tnseq": "true",
+    "tnscope": "true",
+    "varscan": "true"
 }

inputs

@@ -25,7 +25,7 @@
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}",
   "{{ project_name }}.germline": {{ germline }},
-  "{{ project_name }}.TNseq": {{ TNseq }},
-  "{{ project_name }}.TNscope": {{ TNscope }},
-  "{{ project_name }}.Varscan": {{ Varscan }}
+  "{{ project_name }}.tnseq": {{ tnseq }},
+  "{{ project_name }}.tnscope": {{ tnscope }},
+  "{{ project_name }}.varscan": {{ varscan }}
 }

workflow.wdl

@@ -47,9 +47,9 @@ workflow {{ project_name }} {
 	String? cosmic_vcf
 
 	Boolean germline
-	Boolean TNseq
-	Boolean TNscope
-	Boolean Varscan
+	Boolean tnseq
+	Boolean tnscope
+	Boolean varscan
 
 
 	call mapping.mapping as tumor_mapping {
@@ -275,7 +275,7 @@ workflow {{ project_name }} {
 		cluster_config=cluster_config
 	}
 	
-	if (TNseq) {
+	if (tnseq) {
 		call TNseq.TNseq as TNseq {
 			input:
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
@@ -319,7 +319,7 @@ workflow {{ project_name }} {
 		}
 	}
 
-	if (TNscope) {
+	if (tnscope) {
 		call TNscope.TNscope as TNscope {
 			input:
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
@@ -363,7 +363,7 @@ workflow {{ project_name }} {
 		}
 	}
 
-	if (Varscan) {
+	if (varscan) {
 		call somatic.somatic as somatic {
 			input:
 			sample=sample_id,