From 703b954e3734e34829881eb795b7c53bb296d629 Mon Sep 17 00:00:00 2001
From: Christopher Mohr <christopher.mohr@boehringer-ingelheim.com>
Date: Mon, 11 Dec 2023 15:31:09 +0100
Subject: [PATCH] extend cnv file pattern for read_cnv_data function

---
 R/cnv.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/cnv.R b/R/cnv.R
index dbb0e32..6f560d8 100755
--- a/R/cnv.R
+++ b/R/cnv.R
@@ -41,7 +41,7 @@ new_cnv_output <- function(cnv_file_path, local_app=FALSE) {
 read_cnv_data <- function(cnv_directory, local_app=FALSE){
   cnv_files <- list.files(
     path = cnv_directory,
-    pattern = "*CopyNumberVariants.vcf",
+    pattern = "*cnv.vcf|*CopyNumberVariants.vcf",
     full.names = TRUE
   )
   cnv_data <- map(cnv_files, cnv, local_app)  %>%