from modules.software_base import WorkflowRunnerBase
import os

class FastQCRunner(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="fastqc",
            unneeded_args=["--threads", "-t"],
            output_type=None,
            leaf=True,
            output_for_next_step=False,
            mode=mode
        )

    def find_input_files(self,prev_step_files):
        for line in prev_step_files:
            self.input_file_list.append({
                "id": line["id"],
                "input1": line["output1"],
                "input2": line["output2"],
                "output1": f"{self.output_path}",
                "output2": None,
            })
        if self.leaf:
            return prev_step_files
        else:
            return self.input_file_list

    def build_command_queue(self):
        for item in self.input_file_list:
            base_cmd = [
                self.software_name,
                f"-o {item['output1']}/",
                f"-t {self.threads}",
                self.additional_args
            ]

            # Some specific rules for FastQC
            # depending on the contents of the Manifest file
            if item["input2"]:   # FWD and REV
                base_cmd += [
                    item["input1"], 
                    item["input2"]
                ]
            else:               # FWD only
                base_cmd += [item["input1"]]

            self.command_queue.append(" ".join(base_cmd))