Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison 0.6.1/modules/custom/dump_software_versions/templates/dumpsoftwareversions.py @ 11:749faef1caa9

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
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10:1b9de878b04a 11:749faef1caa9
1 #!/usr/bin/env python
2
3 import yaml
4 import platform
5 import subprocess
6 from textwrap import dedent
7
8
9 def _make_versions_html(versions):
10 html = [
11 dedent(
12 """\\
13 <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"/>
14 <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/pdfmake.min.js"></script>
15 <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/vfs_fonts.js"></script>
16 <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>
17 <style>
18 #cpipes-software-versions tbody:nth-child(even) {
19 background-color: #f2f2f2;
20 }
21 </style>
22 <table class="table" style="width:100%" id="cpipes-software-versions">
23 <thead>
24 <tr>
25 <th> Process Name </th>
26 <th> Software </th>
27 <th> Version </th>
28 </tr>
29 </thead>
30 """
31 )
32 ]
33 for process, tmp_versions in sorted(versions.items()):
34 html.append("<tbody>")
35 for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
36 html.append(
37 dedent(
38 f"""\\
39 <tr>
40 <td><samp>{process if (i == 0) else ''}</samp></td>
41 <td><samp>{tool}</samp></td>
42 <td><samp>{version}</samp></td>
43 </tr>
44 """
45 )
46 )
47 html.append("</tbody>")
48 html.append("</table>")
49 return "\\n".join(html)
50
51
52 versions_this_module = {}
53 versions_this_module["${task.process}"] = {
54 "python": platform.python_version(),
55 "yaml": yaml.__version__,
56 }
57
58 with open("$versions") as f:
59 versions_by_process = yaml.load(f, Loader=yaml.BaseLoader)
60 versions_by_process.update(versions_this_module)
61
62 # aggregate versions by the module name (derived from fully-qualified process name)
63 versions_by_module = {}
64 for process, process_versions in versions_by_process.items():
65 module = process.split(":")[-1]
66 try:
67 assert versions_by_module[module] == process_versions, (
68 "We assume that software versions are the same between all modules. "
69 "If you see this error-message it means you discovered an edge-case "
70 "and should open an issue in nf-core/tools. "
71 )
72 except KeyError:
73 versions_by_module[module] = process_versions
74
75 versions_by_module["CPIPES"] = {
76 "Nextflow": "$workflow.nextflow.version",
77 "$workflow.manifest.name": "$workflow.manifest.version",
78 "${params.pipeline}": "${params.workflow_version}",
79 }
80
81 versions_mqc = {
82 "id": "software_versions",
83 "section_name": "${workflow.manifest.name} Software Versions",
84 "section_href": "https://github.com/CFSAN-Biostatistics/bettercallsal",
85 "plot_type": "html",
86 "description": "Collected at run time from the software output (STDOUT/STDERR).",
87 "data": _make_versions_html(versions_by_module),
88 }
89
90 with open("software_versions.yml", "w") as f:
91 yaml.dump(versions_by_module, f, default_flow_style=False)
92
93 # print('sed -i -e "' + "s%'%%g" + '" *.yml')
94 subprocess.run('sed -i -e "' + "s%'%%g" + '" software_versions.yml', shell=True)
95
96 with open("software_versions_mqc.yml", "w") as f:
97 yaml.dump(versions_mqc, f, default_flow_style=False)
98
99 with open("versions.yml", "w") as f:
100 yaml.dump(versions_this_module, f, default_flow_style=False)