code: def get_pipeline_inputs(job, input_flag, input_file, encryption_key=None, per_file_encryption=False,
                          gdc_download_token=None):
      
      work_dir = os.getcwd()
      job.fileStore.logToMaster('Obtaining file (%s) to the file job store' % input_flag)
      if input_file.startswith(('http', 'https', 'ftp')):
          input_file = get_file_from_url(job, input_file, encryption_key=encryption_key,
                                         per_file_encryption=per_file_encryption,
                                         write_to_jobstore=True)
      elif input_file.startswith(('S3', 's3')):
          input_file = get_file_from_s3(job, input_file, encryption_key=encryption_key,
                                        per_file_encryption=per_file_encryption,
                                        write_to_jobstore=True)
      elif input_file.startswith(('GDC', 'gdc')):
          input_file = get_file_from_gdc(job, input_file, gdc_download_token=gdc_download_token,
                                         write_to_jobstore=True)
      else:
          assert os.path.exists(input_file), 'Bogus Input : ' + input_file
          input_file = job.fileStore.writeGlobalFile(input_file)
      return input_file
docs: Get the input file from s3 or disk and write to file store.
  
      :param str input_flag: The name of the flag
      :param str input_file: The value passed in the config file
      :param str encryption_key: Path to the encryption key if encrypted with sse-c
      :param bool per_file_encryption: If encrypted, was the file encrypted using the per-file method?
      :param str gdc_download_token: The download token to obtain files from the GDC
      :return: fsID for the file
      :rtype: toil.fileStore.FileID