Removed redundant WDLs

broadinstitute · Feb 4, 2025 · bdb3bcc · bdb3bcc
1 parent 9c598ad
commit bdb3bcc
Show file tree

Hide file tree

Showing 4 changed files with 9 additions and 292 deletions.
diff --git a/wdl/CombineVcfsForMakeGq.wdl b/wdl/CombineVcfsForMakeGq.wdl
diff --git a/wdl/PreprocessVcfForVapor.wdl b/wdl/PreprocessVcfForVapor.wdl
diff --git a/wdl/PreprocessVcfForMakeGq.wdl → wdl/ProcessRawCallerVcfForMakeGq.wdl b/wdl/PreprocessVcfForMakeGq.wdl → wdl/ProcessRawCallerVcfForMakeGq.wdl
@@ -1,13 +1,14 @@
 version 1.0
 
-workflow PreprocessVcfForMakeGq {
+workflow ProcessRawCallerVcfForMakeGq {
 	input {
 		String sample_id            # Sample identifier
 		File vcf_path             	# Path to the input VCF file
 
 		File contigs_fai          	# Path to the contigs file
-		File ploidy_table		  	# Path to the ploidy table file
+		File ploidy_table		  			# Path to the ploidy table file
 		Int min_size               	# Minimum size for standardization
+		String caller								# Caller name
 		
 		String sv_pipeline_docker   # Docker image path for GATK-SV
 	}
@@ -18,6 +19,7 @@ workflow PreprocessVcfForMakeGq {
 			vcf_path = vcf_path,
 			contigs_fai = contigs_fai,
 			min_size = min_size,
+			caller = caller,
 			sv_pipeline_docker = sv_pipeline_docker
 	}
 
@@ -41,6 +43,7 @@ task StandardizeVcf {
 		File vcf_path
 		File contigs_fai
 		Int min_size
+		String caller
 		String sv_pipeline_docker
 	}
 
@@ -53,7 +56,7 @@ task StandardizeVcf {
 			--min-size ~{min_size} \
 			~{vcf_path} \
 			~{sample_id}.std.vcf.gz \
-			dragen
+			~{caller}
 
 		tabix -p vcf ~{sample_id}.std.vcf.gz
 	>>>

diff --git a/wdl/Vapor.wdl b/wdl/Vapor.wdl
@@ -26,10 +26,11 @@ workflow Vapor {
 
     RuntimeAttr? runtime_attr_subset_sample
     RuntimeAttr? runtime_attr_vcf_to_bed
+    RuntimeAttr? runtime_attr_preprocess_bed
+    RuntimeAttr? runtime_attr_localize_cram
     RuntimeAttr? runtime_attr_vapor
-    RuntimeAttr? runtime_attr_split_vcf
     RuntimeAttr? runtime_attr_concat_beds
-
+    
     File? NONE_FILE_ # Create a null file - do not use this input
   }