src/toil_lib/files.py
def copy_file_job(job, name, file_id, output_dir):
    """
    Job version of move_files for one file

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str name: Name of output file (including extension)
    :param str file_id: FileStoreID of file
    :param str output_dir: Location to place output file
    """
    work_dir = job.fileStore.getLocalTempDir()
    fpath = job.fileStore.readGlobalFile(file_id, os.path.join(work_dir, name))
    copy_files([fpath], output_dir)
def copy_file_job(job, name, file_id, output_dir):
    """
    Job version of move_files for one file

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str name: Name of output file (including extension)
    :param str file_id: FileStoreID of file
    :param str output_dir: Location to place output file
    """
    work_dir = job.fileStore.getLocalTempDir()
    fpath = job.fileStore.readGlobalFile(file_id, os.path.join(work_dir, name))
    copy_files([fpath], output_dir)
Job version of move_files for one file

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str name: Name of output file (including extension)
    :param str file_id: FileStoreID of file
    :param str output_dir: Location to place output file