taxprofiler/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py

#!/usr/bin/env python

import yaml
import platform
from textwrap import dedent


def _make_versions_html(versions):
    html = [
        dedent(
            """\\
            <style>
            #nf-core-versions tbody:nth-child(even) {
                background-color: #f2f2f2;
            }
            </style>
            <table class="table" style="width:100%" id="nf-core-versions">
                <thead>
                    <tr>
                        <th> Process Name </th>
                        <th> Software </th>
                        <th> Version  </th>
                    </tr>
                </thead>
            """
        )
    ]
    for process, tmp_versions in sorted(versions.items()):
        html.append("<tbody>")
        for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
            html.append(
                dedent(
                    f"""\\
                    <tr>
                        <td><samp>{process if (i == 0) else ''}</samp></td>
                        <td><samp>{tool}</samp></td>
                        <td><samp>{version}</samp></td>
                    </tr>
                    """
                )
            )
        html.append("</tbody>")
    html.append("</table>")
    return "\\n".join(html)


versions_this_module = {}
versions_this_module["${task.process}"] = {
    "python": platform.python_version(),
    "yaml": yaml.__version__,
}

with open("$versions") as f:
    versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module

# aggregate versions by the module name (derived from fully-qualified process name)
versions_by_module = {}
for process, process_versions in versions_by_process.items():
    module = process.split(":")[-1]
    try:
        if versions_by_module[module] != process_versions:
            raise AssertionError(
                "We assume that software versions are the same between all modules. "
                "If you see this error-message it means you discovered an edge-case "
                "and should open an issue in nf-core/tools. "
            )
    except KeyError:
        versions_by_module[module] = process_versions

versions_by_module["Workflow"] = {
    "Nextflow": "$workflow.nextflow.version",
    "$workflow.manifest.name": "$workflow.manifest.version",
}

versions_mqc = {
    "id": "software_versions",
    "section_name": "${workflow.manifest.name} Software Versions",
    "section_href": "https://github.com/${workflow.manifest.name}",
    "plot_type": "html",
    "description": "are collected at run time from the software output.",
    "data": _make_versions_html(versions_by_module),
}

with open("software_versions.yml", "w") as f:
    yaml.dump(versions_by_module, f, default_flow_style=False)
with open("software_versions_mqc.yml", "w") as f:
    yaml.dump(versions_mqc, f, default_flow_style=False)

with open("versions.yml", "w") as f:
    yaml.dump(versions_this_module, f, default_flow_style=False)