Mercurial > repos > kkonganti > hfp_nowayout

comparison 0.5.0/modules/custom/dump_software_versions/templates/dumpsoftwareversions.py @ 0:97cd2f532efe

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:97cd2f532efe
1 #!/usr/bin/env python
2
3 import platform
4 import subprocess
5 from textwrap import dedent
6
7 import yaml
8
9
10 def _make_versions_html(versions):
11 html = [
12 dedent(
13 """\\
14 <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"/>
15 <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/pdfmake.min.js"></script>
16 <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/vfs_fonts.js"></script>
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>
18 <style>
19 #cpipes-software-versions tbody:nth-child(even) {
20 background-color: #f2f2f2;
21 }
22 </style>
23 <table class="table" style="width:100%" id="cpipes-software-versions">
24 <thead>
25 <tr>
26 <th> Process Name </th>
27 <th> Software </th>
28 <th> Version </th>
29 </tr>
30 </thead>
31 """
32 )
33 ]
34 for process, tmp_versions in sorted(versions.items()):
35 html.append("<tbody>")
36 for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
37 html.append(
38 dedent(
39 f"""\\
40 <tr>
41 <td><samp>{process if (i == 0) else ''}</samp></td>
42 <td><samp>{tool}</samp></td>
43 <td><samp>{version}</samp></td>
44 </tr>
45 """
46 )
47 )
48 html.append("</tbody>")
49 html.append("</table>")
50 return "\\n".join(html)
51
52
53 versions_this_module = {}
54 versions_this_module["${task.process}"] = {
55 "python": platform.python_version(),
56 "yaml": yaml.__version__,
57 }
58
59 with open("$versions") as f:
60 versions_by_process = yaml.load(f, Loader=yaml.BaseLoader)
61 versions_by_process.update(versions_this_module)
62
63 # aggregate versions by the module name (derived from fully-qualified process name)
64 versions_by_module = {}
65 for process, process_versions in versions_by_process.items():
66 module = process.split(":")[-1]
67 try:
68 assert versions_by_module[module] == process_versions, (
69 "We assume that software versions are the same between all modules. "
70 "If you see this error-message it means you discovered an edge-case "
71 "and should open an issue in nf-core/tools. "
72 )
73 except KeyError:
74 versions_by_module[module] = process_versions
75
76 versions_by_module["CPIPES"] = {
77 "Nextflow": "$workflow.nextflow.version",
78 "$workflow.manifest.name": "$workflow.manifest.version",
79 "${params.pipeline}": "${params.workflow_version}",
80 }
81
82 versions_mqc = {
83 "id": "software_versions",
84 "section_name": "${workflow.manifest.name} Software Versions",
85 "section_href": "https://cfsan-git.fda.gov/Kranti.Konganti/${workflow.manifest.name.toLowerCase()}",
86 "plot_type": "html",
87 "description": "Collected at run time from the software output (STDOUT/STDERR).",
88 "data": _make_versions_html(versions_by_module),
89 }
90
91 with open("software_versions.yml", "w") as f:
92 yaml.dump(versions_by_module, f, default_flow_style=False)
93
94 # print('sed -i -e "' + "s%'%%g" + '" *.yml')
95 subprocess.run('sed -i -e "' + "s%'%%g" + '" software_versions.yml', shell=True)
96
97 with open("software_versions_mqc.yml", "w") as f:
98 yaml.dump(versions_mqc, f, default_flow_style=False)
99
100 with open("versions.yml", "w") as f:
101 yaml.dump(versions_this_module, f, default_flow_style=False)