From 9962398cb81a56dabc497b5d3f4025d1554f6d05 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 8 Jul 2024 21:10:01 +0000
Subject: Pass output directory to R/qtl script instead of pulling it from the
 environment

Also fixes issue where the control marker keyword was wrong
---
 gn3/api/rqtl.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gn3/api')

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 70ebe12..ae0110d 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -25,11 +25,11 @@ run the rqtl_wrapper script and return the results as JSON
         raise FileNotFoundError
 
     # Split kwargs by those with values and boolean ones that just convert to True/False
-    kwargs = ["covarstruct", "model", "method", "nperm", "scale", "control_marker"]
+    kwargs = ["covarstruct", "model", "method", "nperm", "scale", "control"]
     boolean_kwargs = ["addcovar", "interval", "pstrata", "pairscan"]
     all_kwargs = kwargs + boolean_kwargs
 
-    rqtl_kwargs = {"geno": genofile, "pheno": phenofile}
+    rqtl_kwargs = {"geno": genofile, "pheno": phenofile, "outdir": current_app.config.get("TMPDIR")}
     rqtl_bool_kwargs = []
     for kwarg in all_kwargs:
         if kwarg in request.form:
-- 
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