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-rw-r--r--scripts/rqtl2_wrapper.R2
1 files changed, 1 insertions, 1 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R
index cdbbd17..ab3fa3e 100644
--- a/scripts/rqtl2_wrapper.R
+++ b/scripts/rqtl2_wrapper.R
@@ -330,7 +330,7 @@ generate_lod_plot <- function(cross, scan_result, method, base_dir = ".") {
 }
 
 
-lod_plot_path <- generate_lod_plot(dataset, scan_results, "HK")
+lod_plot_path <- generate_lod_plot(dataset, scan_results, "HK", base_dir=opt$directory)
 lod_plot_path