code: def _convert_fastq(fastq_file, pair_file, rg_name, out_file, config):
      
      out_file = "{0}-fq.mkb".format(os.path.splitext(out_file)[0])
      if not file_exists(out_file):
          with file_transaction(config, out_file) as tx_out_file:
              cl = [config_utils.get_program("mosaik", config,
                                             default="MosaikAligner").replace("Aligner", "Build")]
              cl += ["-q", fastq_file,
                     "-out", tx_out_file,
                     "-st", config["algorithm"].get("platform", "illumina").lower()]
              if pair_file:
                  cl += ["-q2", pair_file]
              if rg_name:
                  cl += ["-id", rg_name]
              env_set = "export MOSAIK_TMP={0}".format(os.path.dirname(tx_out_file))
              subprocess.check_call(env_set + " && " + " ".join(cl), shell=True)
      return out_file
docs: Convert fastq inputs into internal Mosaik representation.