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UBC-Stat-ML · Nov 12, 2024 · 2f4e20c · 2f4e20c
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-11d4beb0
+bebaa4a0
diff --git a/01_intro.html b/01_intro.html
@@ -324,6 +324,7 @@ <h3 class="anchored" data-anchor-id="scientific-workflow">Scientific workflow</h
 </div>
 </div>
 </div>
+<p>In a nutshell, nextflow will submit one or several SLURM job for each node in this graph, gather results, and produce some <a href="report.html">nice</a> <a href="timeline.html">reports</a>.</p>
 </section>
 </section>
 <section id="more-information" class="level2">

diff --git a/10_misc.html b/10_misc.html
@@ -217,6 +217,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#lightweight-code" id="toc-lightweight-code" class="nav-link" data-scroll-target="#lightweight-code">Lightweight code</a></li>
   <li><a href="#library" id="toc-library" class="nav-link" data-scroll-target="#library">Library</a></li>
   </ul></li>
+  <li><a href="#report" id="toc-report" class="nav-link" data-scroll-target="#report">Report</a></li>
   </ul>
 </nav>
     </div>
@@ -550,9 +551,14 @@ <h3 class="anchored" data-anchor-id="library">Library</h3>
 <span id="cb14-55"><a href="#cb14-55" aria-hidden="true" tabindex="-1"></a>    <span class="cf">return</span> <span class="st">"#!/usr/bin/env julia --threads=1"</span></span>
 <span id="cb14-56"><a href="#cb14-56" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
+</section>
+</section>
+<section id="report" class="level2">
+<h2 class="anchored" data-anchor-id="report">Report</h2>
+<p>Following the <a href="https://www.nextflow.io/docs/latest/reports.html">nextflow documentation</a>, we have set <code>nextflow.config</code> so that <a href="report.html"><code>report.html</code></a>, <a href="timeline.html"><code>timeline.html</code></a> and <a href="dag.html"><code>dag.html</code></a> are automatically created.</p>
+<p>To preview them in VS Code, add a VS Code Extension allowing html preview, for example <code>Live Server</code>. Then right click on the html file and select <code>Show Preview</code>.</p>
 
 
-</section>
 </section>
 
 </main> <!-- /main -->

diff --git a/dag.html b/dag.html
@@ -0,0 +1,68 @@
+<!--
+  ~ Copyright 2013-2024, Seqera Labs
+  ~
+  ~ Licensed under the Apache License, Version 2.0 (the "License");
+  ~ you may not use this file except in compliance with the License.
+  ~ You may obtain a copy of the License at
+  ~
+  ~     http://www.apache.org/licenses/LICENSE-2.0
+  ~
+  ~ Unless required by applicable law or agreed to in writing, software
+  ~ distributed under the License is distributed on an "AS IS" BASIS,
+  ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  ~ See the License for the specific language governing permissions and
+  ~ limitations under the License.
+  -->
+<html>
+<head>
+<meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
+</head>
+<body>
+<pre class="mermaid" style="text-align: center;">
+flowchart TB
+    subgraph " "
+    v0["julia_env"]
+    v1["toml"]
+    v4["Channel.fromList"]
+    v7["julia_env"]
+    v8["toml"]
+    v12["plot_script"]
+    end
+    v2([instantiate_process])
+    v3([precompile])
+    v5([run_julia])
+    subgraph combine_workflow
+    v9([instantiate_process])
+    v10([precompile])
+    v11([combine_process])
+    end
+    v13([plot])
+    subgraph " "
+    v14["combined_csvs_folder"]
+    v15[" "]
+    end
+    v6(( ))
+    v0 --> v2
+    v1 --> v2
+    v2 --> v3
+    v3 --> v5
+    v3 --> v13
+    v4 --> v5
+    v5 --> v6
+    v7 --> v9
+    v8 --> v9
+    v9 --> v10
+    v10 --> v11
+    v6 --> v11
+    v11 --> v13
+    v12 --> v13
+    v13 --> v15
+    v13 --> v14
+
+</pre>
+<script type="module">
+  import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@10/dist/mermaid.esm.min.mjs';
+  mermaid.initialize({ startOnLoad: true, maxTextSize: Number.MAX_SAFE_INTEGER, maxEdges: Number.MAX_SAFE_INTEGER });
+</script>
+</body>
+</html>
diff --git a/report.html b/report.html
diff --git a/search.json b/search.json
@@ -49,6 +49,16 @@
       "Misc"
     ]
   },
+  {
+    "objectID": "10_misc.html#report",
+    "href": "10_misc.html#report",
+    "title": "Misc",
+    "section": "Report",
+    "text": "Report\nFollowing the nextflow documentation, we have set nextflow.config so that report.html, timeline.html and dag.html are automatically created.\nTo preview them in VS Code, add a VS Code Extension allowing html preview, for example Live Server. Then right click on the html file and select Show Preview.",
+    "crumbs": [
+      "Misc"
+    ]
+  },
   {
     "objectID": "08_containers.html",
     "href": "08_containers.html",
@@ -294,7 +304,7 @@
     "href": "01_intro.html#background",
     "title": "Intro",
     "section": "Background",
-    "text": "Background\n\nScientific workflow\nA scientific workflow is a directed acyclic graph where each node is a process and each edge between node \\(n\\) to \\(n'\\) denote that at least one output of process \\(n\\) is fed as an input to process \\(n'\\).\nHere is an example from a workflow covered later in this tutorial:\n\n\n\n\n\nflowchart TB\n    subgraph \" \"\n    v0[\"julia_env\"]\n    v1[\"toml\"]\n    v4[\"Channel.fromList\"]\n    v7[\"julia_env\"]\n    v8[\"toml\"]\n    v12[\"plot_script\"]\n    end\n    v2([instantiate_process])\n    v3([precompile])\n    v5([run_julia])\n    subgraph combine_workflow\n    v9([instantiate_process])\n    v10([precompile])\n    v11([combine_process])\n    end\n    v13([plot])\n    subgraph \" \"\n    v14[\"combined_csvs_folder\"]\n    v15[\" \"]\n    end\n    v6(( ))\n    v0 --&gt; v2\n    v1 --&gt; v2\n    v2 --&gt; v3\n    v3 --&gt; v5\n    v3 --&gt; v13\n    v4 --&gt; v5\n    v5 --&gt; v6\n    v7 --&gt; v9\n    v8 --&gt; v9\n    v9 --&gt; v10\n    v10 --&gt; v11\n    v6 --&gt; v11\n    v11 --&gt; v13\n    v12 --&gt; v13\n    v13 --&gt; v15\n    v13 --&gt; v14",
+    "text": "Background\n\nScientific workflow\nA scientific workflow is a directed acyclic graph where each node is a process and each edge between node \\(n\\) to \\(n'\\) denote that at least one output of process \\(n\\) is fed as an input to process \\(n'\\).\nHere is an example from a workflow covered later in this tutorial:\n\n\n\n\n\nflowchart TB\n    subgraph \" \"\n    v0[\"julia_env\"]\n    v1[\"toml\"]\n    v4[\"Channel.fromList\"]\n    v7[\"julia_env\"]\n    v8[\"toml\"]\n    v12[\"plot_script\"]\n    end\n    v2([instantiate_process])\n    v3([precompile])\n    v5([run_julia])\n    subgraph combine_workflow\n    v9([instantiate_process])\n    v10([precompile])\n    v11([combine_process])\n    end\n    v13([plot])\n    subgraph \" \"\n    v14[\"combined_csvs_folder\"]\n    v15[\" \"]\n    end\n    v6(( ))\n    v0 --&gt; v2\n    v1 --&gt; v2\n    v2 --&gt; v3\n    v3 --&gt; v5\n    v3 --&gt; v13\n    v4 --&gt; v5\n    v5 --&gt; v6\n    v7 --&gt; v9\n    v8 --&gt; v9\n    v9 --&gt; v10\n    v10 --&gt; v11\n    v6 --&gt; v11\n    v11 --&gt; v13\n    v12 --&gt; v13\n    v13 --&gt; v15\n    v13 --&gt; v14\n\n\n\n\n\n\nIn a nutshell, nextflow will submit one or several SLURM job for each node in this graph, gather results, and produce some nice reports.",
     "crumbs": [
       "Introduction"
     ]

diff --git a/sitemap.xml b/sitemap.xml
@@ -2,7 +2,7 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
   <url>
     <loc>https://UBC-Stat-ML.github.io/nf-nest-doc/10_misc.html</loc>
-    <lastmod>2024-11-12T16:21:01.121Z</lastmod>
+    <lastmod>2024-11-12T16:53:49.978Z</lastmod>
   </url>
   <url>
     <loc>https://UBC-Stat-ML.github.io/nf-nest-doc/08_containers.html</loc>
@@ -22,7 +22,7 @@
   </url>
   <url>
     <loc>https://UBC-Stat-ML.github.io/nf-nest-doc/01_intro.html</loc>
-    <lastmod>2024-11-12T14:26:12.731Z</lastmod>
+    <lastmod>2024-11-12T16:42:17.851Z</lastmod>
   </url>
   <url>
     <loc>https://UBC-Stat-ML.github.io/nf-nest-doc/02_setup.html</loc>

diff --git a/timeline.html b/timeline.html