diff --git a/Snakefile b/Snakefile
index abf04231c3d26bf7256a81ae35edfc7e14cc16ca..97b9553a27dbc1992745da7a259430cbf53486e5 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"