kkonganti@17: #!/usr/bin/env python
kkonganti@17: 
kkonganti@17: import yaml
kkonganti@17: import platform
kkonganti@17: import subprocess
kkonganti@17: from textwrap import dedent
kkonganti@17: 
kkonganti@17: 
kkonganti@17: def _make_versions_html(versions):
kkonganti@17:     html = [
kkonganti@17:         dedent(
kkonganti@17:             """\\
kkonganti@17:             <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/v/dt/jszip-2.5.0/dt-1.12.1/b-2.2.3/b-colvis-2.2.3/b-html5-2.2.3/b-print-2.2.3/fc-4.1.0/r-2.3.0/sc-2.0.6/sb-1.3.3/sp-2.0.1/datatables.min.css"/>
kkonganti@17:             <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/pdfmake.min.js"></script>
kkonganti@17:             <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/vfs_fonts.js"></script>
kkonganti@17:             <script type="text/javascript" src="https://cdn.datatables.net/v/dt/jszip-2.5.0/dt-1.12.1/b-2.2.3/b-colvis-2.2.3/b-html5-2.2.3/b-print-2.2.3/fc-4.1.0/r-2.3.0/sc-2.0.6/sb-1.3.3/sp-2.0.1/datatables.min.js"></script>
kkonganti@17:             <style>
kkonganti@17:             #cpipes-software-versions tbody:nth-child(even) {
kkonganti@17:                 background-color: #f2f2f2;
kkonganti@17:             }
kkonganti@17:             </style>
kkonganti@17:             <table class="table" style="width:100%" id="cpipes-software-versions">
kkonganti@17:                 <thead>
kkonganti@17:                     <tr>
kkonganti@17:                         <th> Process Name </th>
kkonganti@17:                         <th> Software </th>
kkonganti@17:                         <th> Version  </th>
kkonganti@17:                     </tr>
kkonganti@17:                 </thead>
kkonganti@17:             """
kkonganti@17:         )
kkonganti@17:     ]
kkonganti@17:     for process, tmp_versions in sorted(versions.items()):
kkonganti@17:         html.append("<tbody>")
kkonganti@17:         for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
kkonganti@17:             html.append(
kkonganti@17:                 dedent(
kkonganti@17:                     f"""\\
kkonganti@17:                     <tr>
kkonganti@17:                         <td><samp>{process if (i == 0) else ''}</samp></td>
kkonganti@17:                         <td><samp>{tool}</samp></td>
kkonganti@17:                         <td><samp>{version}</samp></td>
kkonganti@17:                     </tr>
kkonganti@17:                     """
kkonganti@17:                 )
kkonganti@17:             )
kkonganti@17:         html.append("</tbody>")
kkonganti@17:     html.append("</table>")
kkonganti@17:     return "\\n".join(html)
kkonganti@17: 
kkonganti@17: 
kkonganti@17: versions_this_module = {}
kkonganti@17: versions_this_module["${task.process}"] = {
kkonganti@17:     "python": platform.python_version(),
kkonganti@17:     "yaml": yaml.__version__,
kkonganti@17: }
kkonganti@17: 
kkonganti@17: with open("$versions") as f:
kkonganti@17:     versions_by_process = yaml.load(f, Loader=yaml.BaseLoader)
kkonganti@17:     versions_by_process.update(versions_this_module)
kkonganti@17: 
kkonganti@17: # aggregate versions by the module name (derived from fully-qualified process name)
kkonganti@17: versions_by_module = {}
kkonganti@17: for process, process_versions in versions_by_process.items():
kkonganti@17:     module = process.split(":")[-1]
kkonganti@17:     try:
kkonganti@17:         assert versions_by_module[module] == process_versions, (
kkonganti@17:             "We assume that software versions are the same between all modules. "
kkonganti@17:             "If you see this error-message it means you discovered an edge-case "
kkonganti@17:             "and should open an issue in nf-core/tools. "
kkonganti@17:         )
kkonganti@17:     except KeyError:
kkonganti@17:         versions_by_module[module] = process_versions
kkonganti@17: 
kkonganti@17: versions_by_module["CPIPES"] = {
kkonganti@17:     "Nextflow": "$workflow.nextflow.version",
kkonganti@17:     "$workflow.manifest.name": "$workflow.manifest.version",
kkonganti@17:     "${params.pipeline}": "${params.workflow_version}",
kkonganti@17: }
kkonganti@17: 
kkonganti@17: versions_mqc = {
kkonganti@17:     "id": "software_versions",
kkonganti@17:     "section_name": "${workflow.manifest.name} Software Versions",
kkonganti@17:     "section_href": "https://github.com/CFSAN-Biostatistics/bettercallsal",
kkonganti@17:     "plot_type": "html",
kkonganti@17:     "description": "Collected at run time from the software output (STDOUT/STDERR).",
kkonganti@17:     "data": _make_versions_html(versions_by_module),
kkonganti@17: }
kkonganti@17: 
kkonganti@17: with open("software_versions.yml", "w") as f:
kkonganti@17:     yaml.dump(versions_by_module, f, default_flow_style=False)
kkonganti@17: 
kkonganti@17: # print('sed -i -e "' + "s%'%%g" + '" *.yml')
kkonganti@17: subprocess.run('sed -i -e "' + "s%'%%g" + '" software_versions.yml', shell=True)
kkonganti@17: 
kkonganti@17: with open("software_versions_mqc.yml", "w") as f:
kkonganti@17:     yaml.dump(versions_mqc, f, default_flow_style=False)
kkonganti@17: 
kkonganti@17: with open("versions.yml", "w") as f:
kkonganti@17:     yaml.dump(versions_this_module, f, default_flow_style=False)