From e41eb3768f2a7b23cb443fca99d46db20e2ac8bf Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Fri, 6 May 2022 12:18:58 +0200
Subject: [PATCH] clean
---
.../templates/dumpsoftwareversions.py~ | 89 -------------------
1 file changed, 89 deletions(-)
delete mode 100644 modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py~
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py~ b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py~
deleted file mode 100644
index be913b7..0000000
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py~
+++ /dev/null
@@ -1,89 +0,0 @@
-#!/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)
--
GitLab