Function shell_tool_command

plugins/ngs-analysis/scripts/ngs_run_utils.py:119–131

(name: str)

def shell_tool_command(name: str) -> str | None:
    resolved = command_path(name)
    if resolved:
        return name
    module_fallbacks = {
        "snakemake": "snakemake",
        "multiqc": "multiqc",
        "cutadapt": "cutadapt",
    }
    module_name = module_fallbacks.get(name)
    if module_name and module_present(module_name):
        return f"{sys.executable} -m {module_name}"
    return None


def run_cmd(cmd: list[str], cwd: Path, timeout: int | None = None) -> dict[str, Any]: