mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-24 12:39:55 +00:00
102 lines
3.3 KiB
Python
Executable file
Generated
102 lines
3.3 KiB
Python
Executable file
Generated
#!/usr/bin/env python
|
|
|
|
|
|
"""Provide functions to merge multiple versions.yml files."""
|
|
|
|
|
|
import platform
|
|
from textwrap import dedent
|
|
|
|
import yaml
|
|
|
|
|
|
def _make_versions_html(versions):
|
|
"""Generate a tabular HTML output of all versions for MultiQC."""
|
|
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)
|
|
|
|
|
|
def main():
|
|
"""Load all version files and generate merged output."""
|
|
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)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|