multiqc_config.py

#!/usr/bin/env python

import os

import yaml


def multiqc_config(self):
    """Make sure basic multiQC plugins are installed and plots are exported
    Basic template:

    .. code-block:: yaml
        report_comment: >
            This report has been generated by the <a href="https://github.com/nf-core/quantms" target="_blank">nf-core/quantms</a>
            analysis pipeline. For information about how to interpret these results, please see the
            <a href="https://nf-co.re/quantms" target="_blank">documentation</a>.
        report_section_order:
            software_versions:
                order: -1000
            nf-core-quantms-summary:
                order: -1001

        export_plots: true
    """
    passed = []
    failed = []

    # Remove field that should be ignored according to the linting config
    ignore_configs = self.lint_config.get("multiqc_config", [])

    fn = os.path.join(self.wf_path, "assets", "multiqc_config.yml")

    # Return a failed status if we can't find the file
    if not os.path.isfile(fn):
        return {"ignored": ["'assets/multiqc_config.yml' not found"]}

    try:
        with open(fn, "r") as fh:
            mqc_yml = yaml.safe_load(fh)
    except Exception as e:
        return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}

    # Check that the report_comment exists and matches
    try:
        if "report_section_order" not in mqc_yml:
            raise AssertionError()
        orders = {}
        summary_plugin_name = f"{self.pipeline_prefix}-{self.pipeline_name}-summary"
        min_plugins = ["software_versions", summary_plugin_name]
        for plugin in min_plugins:
            if plugin not in mqc_yml["report_section_order"]:
                raise AssertionError(f"Section {plugin} missing in report_section_order")
            if "order" not in mqc_yml["report_section_order"][plugin]:
                raise AssertionError(f"Section {plugin} 'order' missing. Must be < 0")
            plugin_order = mqc_yml["report_section_order"][plugin]["order"]
            if plugin_order >= 0:
                raise AssertionError(f"Section {plugin} 'order' must be < 0")

        for plugin in mqc_yml["report_section_order"]:
            if "order" in mqc_yml["report_section_order"][plugin]:
                orders[plugin] = mqc_yml["report_section_order"][plugin]["order"]

        if orders[summary_plugin_name] != min(orders.values()):
            raise AssertionError(f"Section {summary_plugin_name} should have the lowest order")
        orders.pop(summary_plugin_name)
        if orders["software_versions"] != min(orders.values()):
            raise AssertionError("Section software_versions should have the second lowest order")
    except (AssertionError, KeyError, TypeError) as e:
        failed.append(f"'assets/multiqc_config.yml' does not meet requirements: {e}")
    else:
        passed.append("'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.")

    if "report_comment" not in ignore_configs:
        # Check that the minimum plugins exist and are coming first in the summary
        try:
            if "report_comment" not in mqc_yml:
                raise AssertionError()
            if mqc_yml["report_comment"].strip() != (
                f'This report has been generated by the <a href="https://github.com/nf-core/{self.pipeline_name}" '
                f'target="_blank">nf-core/{self.pipeline_name}</a> analysis pipeline. For information about how to '
                f'interpret these results, please see the <a href="https://nf-co.re/{self.pipeline_name}" '
                'target="_blank">documentation</a>.'
            ):
                raise AssertionError()
        except (AssertionError, KeyError, TypeError):
            failed.append("'assets/multiqc_config.yml' does not contain a matching 'report_comment'.")
        else:
            passed.append("'assets/multiqc_config.yml' contains a matching 'report_comment'.")

    # Check that export_plots is activated
    try:
        if "export_plots" not in mqc_yml:
            raise AssertionError()
        if not mqc_yml["export_plots"]:
            raise AssertionError()
    except (AssertionError, KeyError, TypeError):
        failed.append("'assets/multiqc_config.yml' does not contain 'export_plots: true'.")
    else:
        passed.append("'assets/multiqc_config.yml' contains 'export_plots: true'.")

    return {"passed": passed, "failed": failed}