From e61aa16f0bc3dd282060585e655e497fa3d06b49 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 18 May 2021 19:41:01 +0000
Subject: Account for boolean kwargs in compose_rqtl_cmd

---
 gn3/commands.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/gn3/commands.py b/gn3/commands.py
index db32d1f..add715c 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -31,11 +31,18 @@ def compose_gemma_cmd(gemma_wrapper_cmd: str = "gemma-wrapper",
     return cmd
 
 def compose_rqtl_cmd(rqtl_wrapper_cmd: str,
-                     rqtl_wrapper_kwargs: Dict) -> str:
+                     rqtl_wrapper_kwargs: Dict,
+                     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(
         [f"--{key} {val}" for key, val in rqtl_wrapper_kwargs.items()])
 
+    # Add boolean kwargs (kwargs without values)
+    if len(rqtl_wrapper_bool_kwargs):
+        cmd += " "
+        cmd += " ".join([f"--{val}" for val in rqtl_wrapper_bool_kwargs])
+
     return cmd
 
 def queue_cmd(conn: Redis,
-- 
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