flowcraft/generator/utils.py
def get_nextflow_filepath(log_file):
    """Gets the nextflow file path from the nextflow log file. It searches for
    the nextflow run command throughout the file.

    Parameters
    ----------
    log_file : str
        Path for the .nextflow.log file

    Returns
    -------
    str
        Path for the nextflow file
    """

    with open(log_file) as fh:
        # Searches for the first occurence of the nextflow pipeline
        # file name in the .nextflow.log file
        while 1:
            line = fh.readline()
            if not line:
                # file is empty
                raise eh.LogError("Nextflow command path could not be found - Is "
                                 ".nextflow.log empty?")
            try:
                # Regex supports absolute paths and relative paths
                pipeline_path = re.match(".*\s(.*.nf).*", line) \
                    .group(1)
                return pipeline_path
            except AttributeError:
                continue
def get_nextflow_filepath(log_file):
    with open(log_file) as fh:
        # Searches for the first occurence of the nextflow pipeline
        # file name in the .nextflow.log file
        while 1:
            line = fh.readline()
            if not line:
                # file is empty
                raise eh.LogError("Nextflow command path could not be found - Is "
                                 ".nextflow.log empty?")
            try:
                # Regex supports absolute paths and relative paths
                pipeline_path = re.match(".*\s(.*.nf).*", line) \
                    .group(1)
                return pipeline_path
            except AttributeError:
                continue
def get_nextflow_filepath ( log_file ) : with open ( log_file ) as fh : # Searches for the first occurence of the nextflow pipeline # file name in the .nextflow.log file while 1 : line = fh . readline ( ) if not line : # file is empty raise eh . LogError ( "Nextflow command path could not be found - Is " ".nextflow.log empty?" ) try : # Regex supports absolute paths and relative paths pipeline_path = re . match ( ".*\s(.*.nf).*" , line ) . group ( 1 ) return pipeline_path except AttributeError : continue
Gets the nextflow file path from the nextflow log file. It searches for
    the nextflow run command throughout the file.

    Parameters
    ----------
    log_file : str
        Path for the .nextflow.log file

    Returns
    -------
    str
        Path for the nextflow file
Gets the nextflow file path from the nextflow log file . It searches for the nextflow run command throughout the file .