From e2883e55b47f062b2d3d6ae50d6fe533ba8d841d Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 27 Sep 2024 15:41:20 -0500
Subject: Fix Pair-Scan output paths

Related to 4940195460008192b6ca6269e1fb8c172ada4f17c
---
 scripts/rqtl_wrapper.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index fd786cf..31c1277 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -262,9 +262,9 @@ if (!is.null(opt$pairscan)) {
 # Calculate permutations
 if (opt$nperm > 0) {
   if (!is.null(opt$filename)){
-    perm_out_file = file.path(opt$outdir, "output", paste("PERM_", opt$filename, sep = "" ))
+    perm_out_file = file.path(opt$outdir, "gn3", paste("PERM_", opt$filename, sep = "" ))
   } else {
-    perm_out_file = file.path(opt$outdir, "output", paste(pheno_name, "_PERM_", stri_rand_strings(1, 8), sep = ""))
+    perm_out_file = file.path(opt$outdir, "gn3", paste(pheno_name, "_PERM_", stri_rand_strings(1, 8), sep = ""))
   }
 
   if (!is.null(opt$addcovar) || !is.null(opt$control)){
@@ -303,7 +303,7 @@ if (!is.null(opt$addcovar) || !is.null(opt$control)){
 
 verbose_print('Writing results to CSV file\n')
 if (!is.null(opt$pairscan)) {
-  map_out_file = file.path(opt$outdir, "output", paste("MAP_", opt$filename, sep = "" ))
+  map_out_file = file.path(opt$outdir, "gn3", paste("MAP_", opt$filename, sep = "" ))
   write.csv(qtl_results[1], out_file)
   write.csv(qtl_results[2], map_out_file)
 } else {
-- 
cgit v1.2.3