From bf0a8cb22c0cc0c1dfe25740f88a4cb159dd0064 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 25 May 2021 20:27:33 +0000
Subject: Fix R/qtl command and the way keyword arguments are passed

---
 gn3/commands.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gn3/commands.py b/gn3/commands.py
index 255ea1d..14bd295 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -35,10 +35,10 @@ def compose_rqtl_cmd(rqtl_wrapper_cmd: str,
                      rqtl_wrapper_bool_kwargs: list) -> str:
     """Compose a valid R/qtl command given the correct input"""
     # Add kwargs with values
-    cmd = rqtl_wrapper_cmd + " " + " ".join(
+    cmd = f"Rscript { rqtl_wrapper_cmd } " + " ".join(
         [f"--{key} {val}" for key, val in rqtl_wrapper_kwargs.items()])
 
-    # Add boolean kwargs (kwargs without values)
+    # Add boolean kwargs (kwargs that are either on or off, like --interval)
     if rqtl_wrapper_bool_kwargs:
         cmd += " "
         cmd += " ".join([f"--{val}" for val in rqtl_wrapper_bool_kwargs])
-- 
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