From 0bcd03fd6caedd579b818b58d985211f2441b9df Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Wed, 20 Nov 2024 09:54:45 -0800
Subject: [PATCH] Change input to vcf_files intsead of files_to_merge

---
 bcftools_merge.json | 5 ++---
 bcftools_merge.wdl  | 4 ++--
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/bcftools_merge.json b/bcftools_merge.json
index 081d592..9582d4c 100644
--- 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
index dc980a8..1421f23 100644
--- 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 {