flowcraft.generator.process_details module

flowcraft.generator.process_details.colored_print(msg, color_label='white_bold')[source]
This function enables users to add a color to the print. It also enables to pass end_char to print allowing to print several strings in the same line in different prints.
color_string: str

The color code to pass to the function, which enables color change as well as background color change.

msg: str

The actual text to be printed

end_char: str

The character in which each print should finish. By default it will be “


This function handles the dictionary of attributes of each Process class to print to stdout lists of all the components or the components which the user specifies in the -t flag.

procs_dict: dict

A dictionary with the class attributes for all the components (or components that are used by the -t flag), that allow to create both the short_list and detailed_list. Dictionary example: {“abyss”: {‘input_type’: ‘fastq’, ‘output_type’: ‘fasta’, ‘dependencies’: [], ‘directives’: {‘abyss’: {‘cpus’: 4, ‘memory’: ‘{ 5.GB * task.attempt }’, ‘container’: ‘flowcraft/abyss’, ‘version’: ‘2.1.1’, ‘scratch’: ‘true’}}}

flowcraft.generator.process_details.proc_collector(process_map, args, pipeline_string)[source]

Function that collects all processes available and stores a dictionary of the required arguments of each process class to be passed to procs_dict_parser

process_map: dict

The dictionary with the Processes currently available in flowcraft and their corresponding classes as values

args: argparse.Namespace

The arguments passed through argparser that will be access to check the type of list to be printed

pipeline_string: str

the pipeline string