Change input to vcf_files intsead of files_to_merge

UW-GAC · Nov 20, 2024 · 0bcd03f · 0bcd03f
1 parent 5d1a732
commit 0bcd03f
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/bcftools_merge.json b/bcftools_merge.json
@@ -1,10 +1,9 @@
 {
-    "bcftools_merge.files_to_merge": [
+    "bcftools_merge.vcf_files": [
         ["tmp/AMR_subset1000_chr22.vcf.gz", "tmp/EUR_subset1000_chr22.vcf.gz"]
     ],
     "bcftools_merge.output_prefixes": [
         "merged_chr22"
     ],
-    "bcftools_merge.missing_to_ref": false,
-    "bcftools_merge.create_index_files": true
+    "bcftools_merge.missing_to_ref": false
 }
diff --git a/bcftools_merge.wdl b/bcftools_merge.wdl
@@ -3,14 +3,14 @@ version 1.0
 
 workflow bcftools_merge {
     input {
-        Array[Array[File]] files_to_merge
+        Array[Array[File]] vcf_files
         Array[String] output_prefixes
         Boolean missing_to_ref = false
         String? merge_options
         Int mem_gb = 16
     }
 
-    scatter (pair in zip(files_to_merge, output_prefixes)) {
+    scatter (pair in zip(vcf_files, output_prefixes)) {
 
         scatter (vcf_file in pair.left) {
             call create_index_file {