From 8e9af58840d7792391ce1d0dd9d32be51e0e09dd Mon Sep 17 00:00:00 2001
From: Michael Gatzen <mgatzen@broadinstitute.org>
Date: Wed, 18 Sep 2024 16:14:48 -0400
Subject: [PATCH] Removed unused ref_fasta and index

---
 ImputationPipeline/ProGRESSMultivariateRiskModel.wdl | 4 ----
 ImputationPipeline/ScoreBGE/ScoreBGE.wdl             | 2 --
 2 files changed, 6 deletions(-)

diff --git a/ImputationPipeline/ProGRESSMultivariateRiskModel.wdl b/ImputationPipeline/ProGRESSMultivariateRiskModel.wdl
index aebf0dc29..1f9f88f8d 100644
--- a/ImputationPipeline/ProGRESSMultivariateRiskModel.wdl
+++ b/ImputationPipeline/ProGRESSMultivariateRiskModel.wdl
@@ -28,8 +28,6 @@ workflow ProGRESSMultivariateRiskModel {
         String chromosome_encoding = "chrMT"
         Int mem_gb_array_vcf_to_plink = 16
 
-        File ref_fasta
-        File ref_fasta_index
         File ref_dict
     }
 
@@ -42,8 +40,6 @@ workflow ProGRESSMultivariateRiskModel {
             basename = basename,
             weights = prs_weights,
 
-            ref_fasta = ref_fasta,
-            ref_fasta_index = ref_fasta_index,
             ref_dict = ref_dict
     }
 
diff --git a/ImputationPipeline/ScoreBGE/ScoreBGE.wdl b/ImputationPipeline/ScoreBGE/ScoreBGE.wdl
index 148bc6898..45794a1d0 100644
--- a/ImputationPipeline/ScoreBGE/ScoreBGE.wdl
+++ b/ImputationPipeline/ScoreBGE/ScoreBGE.wdl
@@ -56,8 +56,6 @@ task ScoreGvcfAndVcf {
 
         String score_bge_docker = "us.gcr.io/broad-dsde-methods/palantir-workflows-score-bge:palantir-workflows_5feb024"
 
-        File ref_fasta
-        File ref_fasta_index
         File ref_dict
 
         Int preemptible = 1