Snakemake的接口报告插件

本包定义了Snakemake与其报告插件之间的接口。

插件应实现以下框架以符合此接口。建议使用Snakemake的poetry插件在python包中设置此框架（以及自动化测试），请参阅 https://github.com/snakemake/poetry-snakemake-plugin。

from dataclasses import dataclass, field

from snakemake_interface_common.exceptions import WorkflowError
from snakemake_interface_report_plugins.reporter import ReporterBase
from snakemake_interface_report_plugins.settings import ReportSettingsBase


# Optional:
# Define additional settings for your reporter.
# They will occur in the Snakemake CLI as --report-<reporter-name>-<param-name>
# Omit this class if you don't need any.
# Make sure that all defined fields are Optional (or bool) and specify a default value
# of None (or False) or anything else that makes sense in your case.
@dataclass
class ReportSettings(ReportSettingsBase):
    myparam: Optional[int] = field(
        default=None,
        metadata={
            "help": "Some help text",
            # Optionally request that setting is also available for specification
            # via an environment variable. The variable will be named automatically as
            # SNAKEMAKE_REPORT_<reporter-name>_<param-name>, all upper case.
            # This mechanism should ONLY be used for passwords and usernames.
            # For other items, we rather recommend to let people use a profile
            # for setting defaults
            # (https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles).
            "env_var": False,
            # Optionally specify a function that parses the value given by the user.
            # This is useful to create complex types from the user input.
            "parse_func": ...,
            # If a parse_func is specified, you also have to specify an unparse_func
            # that converts the parsed value back to a string.
            "unparse_func": ...,
            # Optionally specify that setting is required when the reporter is in use.
            "required": True,
            # Optionally specify multiple args with "nargs": True
        },
    )


# Required:
# Implementation of your reporter
class Reporter(ReporterBase):
    def __post_init__(self):
        # initialize additional attributes
        # Do not overwrite the __init__ method as this is kept in control of the base
        # class in order to simplify the update process.
        # See https://github.com/snakemake/snakemake-interface-report-plugins/snakemake_interface_report_plugins/reporter.py
        # for attributes of the base class.
        # In particular, the settings of above ReportSettings class are accessible via
        # self.settings.

    def render(self):
        # Render the report, using attributes of the base class.
        ...