--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/modules/custom/dump_software_versions/templates/dumpsoftwareversions.py	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,100 @@
+#!/usr/bin/env python
+
+import yaml
+import platform
+import subprocess
+from textwrap import dedent
+
+
+def _make_versions_html(versions):
+    html = [
+        dedent(
+            """\\
+            <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"/>
+            <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/pdfmake.min.js"></script>
+            <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/vfs_fonts.js"></script>
+            <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>
+            <style>
+            #cpipes-software-versions tbody:nth-child(even) {
+                background-color: #f2f2f2;
+            }
+            </style>
+            <table class="table" style="width:100%" id="cpipes-software-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_by_process.update(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["CPIPES"] = {
+    "Nextflow": "$workflow.nextflow.version",
+    "$workflow.manifest.name": "$workflow.manifest.version",
+    "${params.pipeline}": "${params.workflow_version}",
+}
+
+versions_mqc = {
+    "id": "software_versions",
+    "section_name": "${workflow.manifest.name} Software Versions",
+    "section_href": "https://github.com/CFSAN-Biostatistics/bettercallsal",
+    "plot_type": "html",
+    "description": "Collected at run time from the software output (STDOUT/STDERR).",
+    "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)
+
+# print('sed -i -e "' + "s%'%%g" + '" *.yml')
+subprocess.run('sed -i -e "' + "s%'%%g" + '" software_versions.yml', shell=True)
+
+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)