pipeline/script/run_wdl.py

import argparse
import json
import os
import subprocess
import time


def run(barcode, normal, umi, input_dir, output_dir, project, bed, wdl):
    input_dir = os.path.realpath(input_dir)
    output_dir = os.path.realpath(output_dir)
    wdl = os.path.realpath(wdl)
    arg = {
        "pipeline.tumor": barcode,
        "pipeline.normal": normal,
        "pipeline.umi": umi,
        "pipeline.input_dir": input_dir,
        "pipeline.output_dir": output_dir,
        "pipeline.project": project,
        "pipeline.bed": bed
    }

    arg = {key: value for key, value in arg.items() if value not in (None, '', False)}

    # generate json
    jsfile_path = os.path.join(output_dir, f'{barcode}.json')
    with open(jsfile_path, 'w') as jsfile:
        jsfile.write(json.dumps(arg, indent=4, ensure_ascii=False))

    # run pipeline
    cmd1 = 'export PATH=/home/zhangchao/project/pipeline/workflow/script:$PATH'
    cmd2 = 'export PUBLIC=/home/zhangchao/project/pipeline/workflow/script/public'
    cmd3 = f'cd {output_dir}'

    cmd4 = f'/home/zhangchao/soft/jdk-17.0.7+7/bin/java ' \
           f'-Dconfig.file=/home/zhangchao/project/pipeline/workflow/script/cromwell.examples.conf ' \
           f'-jar /home/zhangchao/soft/cromwell-85.jar run --inputs {jsfile_path} {wdl}'
    cmd = f'{cmd1}; {cmd2}; {cmd3}; {cmd4}'

    # 记录开始时间
    start_time = time.time()
    print(cmd)
    ret = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding="utf-8")
    pidnum = ret.pid
    with open(os.path.join(output_dir, 'pid'), 'w') as pidfile:
        pidfile.write(str(pidnum))
    ret.wait()
    # 记录结束时间
    end_time = time.time()
    # 计算运行时间
    elapsed_time = end_time - start_time

    print("\n运行时间：{:.2f} 秒".format(elapsed_time))

    print(ret.stdout.read(), ret.stderr.read())
    print('#' * 50)
    print('读取日志')


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description="JM to run pipeline")

    parser.add_argument('-n', '--barcode', help="sample's barcode", required=True)
    parser.add_argument('-s', '--normal', help="sample's normal", default='', required=False, nargs='?')
    parser.add_argument('-u', '--umi', action='store_true', help="is umi sample", default=False)
    parser.add_argument('-i', '--input_dir', help="sample's input_dir/workdir", required=True)
    parser.add_argument('-o', '--output_dir', help="Output directory, default ./", default='./')
    parser.add_argument('-p', '--project', help="project", required=True)
    parser.add_argument('-b', '--bed', help="bed", required=True)
    parser.add_argument('-w', '--wdl', help="wdl")

    args = parser.parse_args()

    run(args.barcode, args.normal, args.umi, args.input_dir, args.output_dir, args.project, args.bed, args.wdl)