From 8539c88be5e182958ea70e3634fb2328e66fb98d Mon Sep 17 00:00:00 2001
From: Karim Hajji <karim.hajji@rivm.nl>
Date: Fri, 26 Apr 2024 16:50:38 +0200
Subject: [PATCH] fix: Fix type error doing dryrun with fixed reference

The type of the reference location was a str in stead of pathlib.Path
when doing a dryrun in Snakefile.
---
 Snakefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Snakefile b/Snakefile
index 9a72a69..dee62b7 100644
--- a/Snakefile
+++ b/Snakefile
@@ -41,7 +41,7 @@ mash_db = db_dir.joinpath("bacteria-refseq", "db.msh")
 referenceseeker_md5 = str(db_dir.joinpath("bacteria-refseq", "downloaded_db.txt"))
 
 if (config["dryrun"] is True) and (GIVEN_REF != "None"):
-    ref_genome = GIVEN_REF
+    ref_genome = Path(GIVEN_REF)
 else:
     ref_genome = output_dir.joinpath("ref_genomes_used", "cluster_1", "ref_genome.seq")