mirror of
https://github.com/MillironX/taxprofiler.git
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102 lines
3.3 KiB
Python
Executable file
Generated
102 lines
3.3 KiB
Python
Executable file
Generated
#!/usr/bin/env python
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"""Provide functions to merge multiple versions.yml files."""
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import platform
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from textwrap import dedent
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import yaml
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def _make_versions_html(versions):
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"""Generate a tabular HTML output of all versions for MultiQC."""
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html = [
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dedent(
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"""\\
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<style>
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#nf-core-versions tbody:nth-child(even) {
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background-color: #f2f2f2;
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}
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</style>
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<table class="table" style="width:100%" id="nf-core-versions">
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<thead>
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<tr>
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<th> Process Name </th>
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<th> Software </th>
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<th> Version </th>
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</tr>
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</thead>
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"""
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)
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]
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for process, tmp_versions in sorted(versions.items()):
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html.append("<tbody>")
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for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
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html.append(
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dedent(
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f"""\\
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<tr>
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<td><samp>{process if (i == 0) else ''}</samp></td>
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<td><samp>{tool}</samp></td>
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<td><samp>{version}</samp></td>
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</tr>
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"""
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)
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)
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html.append("</tbody>")
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html.append("</table>")
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return "\\n".join(html)
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def main():
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"""Load all version files and generate merged output."""
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versions_this_module = {}
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versions_this_module["${task.process}"] = {
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"python": platform.python_version(),
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"yaml": yaml.__version__,
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}
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with open("$versions") as f:
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versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
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# aggregate versions by the module name (derived from fully-qualified process name)
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versions_by_module = {}
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for process, process_versions in versions_by_process.items():
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module = process.split(":")[-1]
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try:
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if versions_by_module[module] != process_versions:
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raise AssertionError(
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"We assume that software versions are the same between all modules. "
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"If you see this error-message it means you discovered an edge-case "
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"and should open an issue in nf-core/tools. "
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)
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except KeyError:
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versions_by_module[module] = process_versions
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versions_by_module["Workflow"] = {
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"Nextflow": "$workflow.nextflow.version",
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"$workflow.manifest.name": "$workflow.manifest.version",
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}
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versions_mqc = {
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"id": "software_versions",
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"section_name": "${workflow.manifest.name} Software Versions",
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"section_href": "https://github.com/${workflow.manifest.name}",
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"plot_type": "html",
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"description": "are collected at run time from the software output.",
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"data": _make_versions_html(versions_by_module),
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}
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with open("software_versions.yml", "w") as f:
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yaml.dump(versions_by_module, f, default_flow_style=False)
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with open("software_versions_mqc.yml", "w") as f:
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yaml.dump(versions_mqc, f, default_flow_style=False)
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with open("versions.yml", "w") as f:
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yaml.dump(versions_this_module, f, default_flow_style=False)
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if __name__ == "__main__":
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main()
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