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