diff options
| -rw-r--r-- | gn3/computations/rqtl2.py | 17 |
1 files changed, 17 insertions, 0 deletions
diff --git a/gn3/computations/rqtl2.py b/gn3/computations/rqtl2.py index 6e8e06a..bccedc0 100644 --- a/gn3/computations/rqtl2.py +++ b/gn3/computations/rqtl2.py @@ -49,3 +49,20 @@ def validate_required_keys(required_keys:list, data:dict) -> tuple[bool, str]: return False, f"Required key(s) missing: {', '.join(missing_keys)}" return True, "" + +def compose_rqtl2_cmd(rqtl_path, input_file, + output_file, workspace_dir, + data, config): + """Compose the command for running the R/QTL2 analysis.""" + # pylint: disable=R0913 + params = { + "input_file": input_file, + "directory": workspace_dir, + "output_file": output_file, + "nperm": data.get("nperm", 0), + "threshold": data.get("threshold", 1), + "cores": config.get('MULTIPROCESSOR_PROCS', 1) + } + rscript_path = config.get("RSCRIPT", "Rscript") + return f"{rscript_path} { rqtl_path } " + " ".join( + [f"--{key} {val}" for key, val in params.items()]) |