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-rw-r--r--gn3/commands.py9
1 files changed, 8 insertions, 1 deletions
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,