clean

modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py~

-#!/usr/bin/env python
-
-import yaml
-import platform
-from textwrap import dedent
-
-
-def _make_versions_html(versions):
-    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)
-
-
-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:
-        assert versions_by_module[module] == process_versions, (
-            "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)