#!/usr/bin/env python

"""MultiQC example plugin functions

We can add any custom Python functions here and call them

using the setuptools plugin hooks.

"""

from __future__ import print_function

from multiqc import config, report

import importlib_metadata

import logging

# Initialise the main MultiQC logger

log = logging.getLogger("multiqc")

# Add default config options for the things that are used in MultiQC_NGI

def example_plugin_execution_start():

"""Code to execute after the config files and

command line flags have been parsedself.

This setuptools hook is the earliest that will be able

to use custom command line flags.

"""

# Halt execution if we've disabled the plugin

if config.kwargs.get("disable_plugin", True):

return None

# Plugin's version number defined in pyproject.toml:

version = importlib_metadata.version("multiqc_example_plugin")

log.info("Running Example MultiQC Plugin v{}".format(version))

# Add to the main MultiQC config object.

# User config files have already been loaded at this point

# so we check whether the value is already set. This is to avoid

# clobbering values that have been customised by users.

# Add to the search patterns used by modules

if "my_example/key_value_pairs" not in config.sp:

config.update_dict(config.sp, {"my_example/key_value_pairs": {"fn": "my_plugin_output.tsv"}})

if "my_example/plot_data" not in config.sp:

config.update_dict(config.sp, {"my_example/plot_data": {"fn": "my_plugin_plotdata.tsv"}})

# Some additional filename cleaning

config.fn_clean_exts.extend([".my_tool_extension", ".removeMetoo"])

# Ignore some files generated by the custom pipeline

config.fn_ignore_paths.extend(

[

"*/my_awesome_pipeline/fake_news/*",

"*/my_awesome_pipeline/red_herrings/*",

"*/my_awesome_pipeline/noisy_data/*",

"*/my_awesome_pipeline/rubbish/*",

]

)