context to track

broadinstitute · Nov 25, 2024 · 2a39fcb · 2a39fcb
1 parent 1e936a6
commit 2a39fcb
Showing 1 changed file with 10 additions and 10 deletions.
diff --git a/wdl/CombineBatches.wdl b/wdl/CombineBatches.wdl
@@ -35,8 +35,8 @@ workflow CombineBatches {
     File stratification_config_part2
     # These arrays give the names and intervals for reference contexts for stratification (same lengths)
     # Names must correspond to those in the stratification config files
-    Array[String] context_names
-    Array[File] context_bed_files
+    Array[String] track_names
+    Array[File] track_bed_files
 
     File reference_fasta
     File reference_fasta_fai
@@ -195,8 +195,8 @@ workflow CombineBatches {
         reference_dict=reference_dict,
         clustering_config=clustering_config_part1,
         stratification_config=stratification_config_part1,
-        context_bed_files=context_bed_files,
-        context_names=context_names,
+        track_bed_files=track_bed_files,
+        track_names=track_names,
         breakpoint_summary_strategy="REPRESENTATIVE",
         java_mem_fraction=java_mem_fraction,
         gatk_docker=gatk_docker,
@@ -214,8 +214,8 @@ workflow CombineBatches {
         reference_dict=reference_dict,
         clustering_config=clustering_config_part2,
         stratification_config=stratification_config_part2,
-        context_bed_files=context_bed_files,
-        context_names=context_names,
+        track_bed_files=track_bed_files,
+        track_names=track_names,
         breakpoint_summary_strategy="REPRESENTATIVE",
         java_mem_fraction=java_mem_fraction,
         gatk_docker=gatk_docker,
@@ -328,8 +328,8 @@ task GroupedSVClusterTask {
 
     File clustering_config
     File stratification_config
-    Array[File] context_bed_files
-    Array[String] context_names
+    Array[File] track_bed_files
+    Array[String] track_names
 
     Float context_overlap_frac = 0
     Int context_num_breakpoint_overlaps = 1
@@ -388,8 +388,8 @@ task GroupedSVClusterTask {
       -O ~{output_prefix}.vcf.gz \
       --clustering-config ~{clustering_config} \
       --stratify-config ~{stratification_config} \
-      --context-intervals ~{sep=" --context-intervals " context_bed_files} \
-      --context-name ~{sep=" --context-name " context_names} \
+      --track-intervals ~{sep=" --track-intervals " track_bed_files} \
+      --track-name ~{sep=" --track-name " track_names} \
       --stratify-overlap-fraction ~{context_overlap_frac} \
       --stratify-num-breakpoint-overlaps ~{context_num_breakpoint_overlaps} \
       --stratify-num-breakpoint-overlaps-interchromosomal ~{context_interchrom_num_breakpoint_overlaps} \