flowcraft/templates/skesa.py
def main(sample_id, fastq_pair, clear):
    """Main executor of the skesa template.

    Parameters
    ----------
    sample_id : str
        Sample Identification string.
    fastq_pair : list
        Two element list containing the paired FastQ files.
    clear : str
        Can be either 'true' or 'false'. If 'true', the input fastq files will
        be removed at the end of the run, IF they are in the working directory
    """

    logger.info("Starting skesa")

    # Determine output file
    if "_trim." in fastq_pair[0]:
        sample_id += "_trim"
    version = __get_version_skesa()["version"]
    output_file = "{}_skesa{}.fasta".format(sample_id, version.replace(".", ""))

    cli = [
        "skesa",
        "--fastq",
        "{},{}".format(fastq_pair[0], fastq_pair[1]),
        "--gz",
        "--use_paired_ends",
        "--cores",
        "${task.cpus}"
    ]

    logger.debug("Running Skesa subprocess with command: {}".format(cli))

    with open(output_file, "w") as fh:
        p = subprocess.Popen(cli, stdout=fh, stderr=PIPE)
    stdout, stderr = p.communicate()

    # Attempt to decode STDERR output from bytes. If unsuccessful, coerce to
    # string
    try:
        stderr = stderr.decode("utf8")
        stdout = stdout.decode("utf8")
    except (UnicodeDecodeError, AttributeError):
        stderr = str(stderr)
        stdout = str(stdout)

    logger.info("Finished Skesa subprocess with STDOUT:\\n"
                "======================================\\n{}".format(stdout))
    logger.info("Fished Skesa subprocess with STDERR:\\n"
                "======================================\\n{}".format(stderr))
    logger.info("Finished Skesa with return code: {}".format(
        p.returncode))

    # Remove input fastq files when clear option is specified.
    # Only remove temporary input when the expected output exists.
    if clear == "true" and os.path.exists(output_file):
        clean_up(fastq_pair)

    with open(".status", "w") as fh:
        if p.returncode != 0:
            fh.write("error")
            raise SystemExit(p.returncode)
        else:
            fh.write("pass")
def main(sample_id, fastq_pair, clear):
    logger.info("Starting skesa")

    # Determine output file
    if "_trim." in fastq_pair[0]:
        sample_id += "_trim"
    version = __get_version_skesa()["version"]
    output_file = "{}_skesa{}.fasta".format(sample_id, version.replace(".", ""))

    cli = [
        "skesa",
        "--fastq",
        "{},{}".format(fastq_pair[0], fastq_pair[1]),
        "--gz",
        "--use_paired_ends",
        "--cores",
        "${task.cpus}"
    ]

    logger.debug("Running Skesa subprocess with command: {}".format(cli))

    with open(output_file, "w") as fh:
        p = subprocess.Popen(cli, stdout=fh, stderr=PIPE)
    stdout, stderr = p.communicate()

    # Attempt to decode STDERR output from bytes. If unsuccessful, coerce to
    # string
    try:
        stderr = stderr.decode("utf8")
        stdout = stdout.decode("utf8")
    except (UnicodeDecodeError, AttributeError):
        stderr = str(stderr)
        stdout = str(stdout)

    logger.info("Finished Skesa subprocess with STDOUT:\\n"
                "======================================\\n{}".format(stdout))
    logger.info("Fished Skesa subprocess with STDERR:\\n"
                "======================================\\n{}".format(stderr))
    logger.info("Finished Skesa with return code: {}".format(
        p.returncode))

    # Remove input fastq files when clear option is specified.
    # Only remove temporary input when the expected output exists.
    if clear == "true" and os.path.exists(output_file):
        clean_up(fastq_pair)

    with open(".status", "w") as fh:
        if p.returncode != 0:
            fh.write("error")
            raise SystemExit(p.returncode)
        else:
            fh.write("pass")
def main ( sample_id , fastq_pair , clear ) : logger . info ( "Starting skesa" ) # Determine output file if "_trim." in fastq_pair [ 0 ] : sample_id += "_trim" version = __get_version_skesa ( ) [ "version" ] output_file = "{}_skesa{}.fasta" . format ( sample_id , version . replace ( "." , "" ) ) cli = [ "skesa" , "--fastq" , "{},{}" . format ( fastq_pair [ 0 ] , fastq_pair [ 1 ] ) , "--gz" , "--use_paired_ends" , "--cores" , "${task.cpus}" ] logger . debug ( "Running Skesa subprocess with command: {}" . format ( cli ) ) with open ( output_file , "w" ) as fh : p = subprocess . Popen ( cli , stdout = fh , stderr = PIPE ) stdout , stderr = p . communicate ( ) # Attempt to decode STDERR output from bytes. If unsuccessful, coerce to # string try : stderr = stderr . decode ( "utf8" ) stdout = stdout . decode ( "utf8" ) except ( UnicodeDecodeError , AttributeError ) : stderr = str ( stderr ) stdout = str ( stdout ) logger . info ( "Finished Skesa subprocess with STDOUT:\\n" "======================================\\n{}" . format ( stdout ) ) logger . info ( "Fished Skesa subprocess with STDERR:\\n" "======================================\\n{}" . format ( stderr ) ) logger . info ( "Finished Skesa with return code: {}" . format ( p . returncode ) ) # Remove input fastq files when clear option is specified. # Only remove temporary input when the expected output exists. if clear == "true" and os . path . exists ( output_file ) : clean_up ( fastq_pair ) with open ( ".status" , "w" ) as fh : if p . returncode != 0 : fh . write ( "error" ) raise SystemExit ( p . returncode ) else : fh . write ( "pass" )
Main executor of the skesa template.

    Parameters
    ----------
    sample_id : str
        Sample Identification string.
    fastq_pair : list
        Two element list containing the paired FastQ files.
    clear : str
        Can be either 'true' or 'false'. If 'true', the input fastq files will
        be removed at the end of the run, IF they are in the working directory
Main executor of the skesa template .