From f2a641a0e2a645ee24a1a5f2126d8f19630f2a3d Mon Sep 17 00:00:00 2001
From: Lasse Ebdrup Pedersen <6593035+cfblaeb@users.noreply.github.com>
Date: Mon, 18 Dec 2023 17:57:00 +0100
Subject: [PATCH] Update Snakefile to work with current medaka

medaka has a different syntax that the current snakefile expects
---
 Snakefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Snakefile b/Snakefile
index 409c509..3492438 100644
--- a/Snakefile
+++ b/Snakefile
@@ -276,7 +276,7 @@ rule polish_clusters:
     shell:
         """
         rm -rf {output.FOLDER}
-        medaka smolecule --threads {threads} --length 50 --depth 2 --model {params.medaka_model} --method spoa {input.I2} {output.FOLDER} 2> {output.BAM}_smolecule.log
+        medaka smolecule --threads {threads} --length 50 --depth 2 --model {params.medaka_model} --method spoa {output.FOLDER} {input.I2} 2> {output.BAM}_smolecule.log
         cp {output.FOLDER}/consensus.fasta {output.F}
         cp {output.FOLDER}/subreads_to_spoa.bam {output.BAM} && cp {output.FOLDER}/subreads_to_spoa.bam.bai {output.BAM}.bai
         """