From b4c898d8af9f29c431f52772a93385e18d415ca5 Mon Sep 17 00:00:00 2001
From: Rachel  LEGENDRE <rachel.legendre@pasteur.fr>
Date: Mon, 16 Jan 2023 10:03:20 +0100
Subject: [PATCH] change multiqc working directory

---
 Snakefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Snakefile b/Snakefile
index abf0423..97b9553 100755
--- a/Snakefile
+++ b/Snakefile
@@ -466,7 +466,7 @@ if config["kallisto"]["do"]:
 # MultiQC report
 #----------------------------------
 multiqc_input = final_output
-multiqc_input_dir = "."
+multiqc_input_dir = analysis_dir
 multiqc_logs = os.path.join(analysis_dir, "05-Multiqc/multiqc.log")
 multiqc_output = os.path.join(analysis_dir, "05-Multiqc/multiqc_report.html")
 multiqc_options = config['multiqc']['options'] + " -c config/multiqc_config.yaml" 
-- 
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