from modules.software_base import WorkflowRunnerBase
import os

class MapDamageRunner(WorkflowRunnerBase):
    def __init__(self, logger, manifest_list, input_path, output_path="", additional_args="", threads=2, stepname="", mode=None):
        super().__init__(
            logger=logger,
            manifest_list=manifest_list,
            input_path=input_path,
            output_path=output_path,
            additional_args=additional_args,
            threads=threads,
            stepname=stepname,
            software_name="runMapDamage.py",
            unneeded_args=["-i", "-o", "-t", "--input_dir", "--output_dir","--threads"],
            output_type="dir",
            rescan_output=False,
            mode=mode
        )

    def find_input_files(self,prev_step_files):
        return None

    def build_command_queue(self):
        cmd = [
            self.software_name,
            f"--input_dir {self.input_path}",
            f"--output_dir {self.output_path}",
            f"--threads {self.threads}",
            f"{self.additional_args}"
        ]
        
        self.command_queue.append(" ".join(cmd))