See common-workflow-language/cwl-website@274c2bb from refs/heads/main

cwl-bot · cwl-bot · commit 063d788df84c · 2024-05-22T07:53:26.000Z
diff --git a/draft-3/CommandLineTool.html b/draft-3/CommandLineTool.html
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-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
 <link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
 
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-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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diff --git a/draft-3/Workflow.html b/draft-3/Workflow.html
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-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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diff --git a/draft-3/index.html b/draft-3/index.html
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-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
 <link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
 
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diff --git a/features/index.html b/features/index.html
@@ -182,7 +182,7 @@ <h2 id="parallelization-and-scale-with-cwl">
 is determined by the dependencies between steps. Workflow steps which do not
 depend on one another may run in parallel.</p>
 
-<p>Additionally, the <strong><a href="https://www.commonwl.org/user_guide/23-scatter-workflow/index.html">scatter</a></strong> feature in CWL allows the repeated execution of a CWL step in parallel (depending on the resources available) over a list of inputs.  This can be done without requiring the modification of the underlying tool description.</p>
+<p>Additionally, the <strong><a href="https://www.commonwl.org/user_guide/topics/workflows.html#scattering-steps">scatter</a></strong> feature in CWL allows the repeated execution of a CWL step in parallel (depending on the resources available) over a list of inputs.  This can be done without requiring the modification of the underlying tool description.</p>
 
 <p>By design, the CWL standards do not impose any technical limitations to the size of files processed or to the number of tasks run in parallel. The major scalability bottlenecks are hardware-related — not having enough machines with enough memory, compute or disk space to process more and more data at a larger scale. As these boundaries move in the future with technological advances, the CWL standards should be able to keep up and not be a cause of limitations.</p>
 
diff --git a/getting-started/index.html b/getting-started/index.html
@@ -95,9 +95,9 @@ <h1 class="post-title col-lg-10">
     <div class="getting-started"><p>Below are some useful resources to getting started.  Additionally, help is available through <a href="/community">community resources</a> such as the <a href="https://matrix.to/#/#common-workflow-language_common-workflow-language:gitter.im">CWL Matrix channel</a>.</p>
 
 <ul>
-  <li>Learn to write CWL using the <a href="/user_guide/">CWL user guide</a> which provides a gentle introduction to creating CWL command line tool and workflow descriptions.</li>
+  <li>Learn to write CWL using the <a href="https://www.commonwl.org/user_guide/">CWL user guide</a> which provides a gentle introduction to creating CWL command line tool and workflow descriptions.</li>
   <li>Browse <a href="/implementations/">CWL Implementations</a> to find a software package that’s right for you.</li>
-  <li>Follow <a href="http://www.commonwl.org/user_guide/rec-practices/">CWL Recommended Practices</a> to make your CWL tools and workflows more efficient, reusable and transparent.</li>
+  <li>Follow <a href="https://www.commonwl.org/user_guide/topics/best-practices.html#best-practices">CWL Recommended Practices</a> to make your CWL tools and workflows more efficient, reusable and transparent.</li>
   <li>Read <a href="https://github.com/pitagora-galaxy/cwl/wiki/CWL-Start-Guide-JP" lang="ja" hreflang="ja">CWLの日本語での解説ドキュメント</a>  a 15 minute introduction to the CWL project in Japanese.</li>
   <li>Watch a series of <a href="https://stepik.org/lesson/35918/step/1?unit=15070">video lessons about CWL</a> in Russian as part of the <a href="https://stepik.org/course/1612/syllabus" lang="ru">Управление вычислениями</a> (Computation Management) free online course.</li>
   <li>Find <a href="https://github.com/common-workflow-library/bio-cwl-tools">CWL descriptions for life-science tools</a> to use directly or incorporate into your workflows.</li>
diff --git a/tools/index.html b/tools/index.html
@@ -454,7 +454,7 @@ <h3 id="specs">
     </tr>
     <tr>
       <td><a href="https://edamontology.org/">EDAM</a></td>
-      <td>Ontology for categorizing operations and formats, useful in <a href="https://www.commonwl.org/user_guide/17-metadata/">CWL metadata</a>. Primarily used in bioscientific domains.</td>
+      <td>Ontology for categorizing operations and formats, useful in <a href="https://www.commonwl.org/user_guide/topics/metadata-and-authorship.html#metadata-and-authorship">CWL metadata</a>. Primarily used in bioscientific domains.</td>
     </tr>
     <tr>
       <td><a href="https://schema.org/">schema.org</a></td>
diff --git a/v1.0/CommandLineTool.html b/v1.0/CommandLineTool.html
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-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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 <link rel="shortcut icon"
-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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 <link rel="shortcut icon"
-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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 <link rel="shortcut icon"
-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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 <link rel="shortcut icon"
-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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 <link rel="shortcut icon"
-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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 <link rel="shortcut icon"
-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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 <link rel="shortcut icon"
-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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 <link rel="stylesheet" href="/assets/styles-fix.css" />
 <link rel="shortcut icon"
-href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
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@@ -122,8 +122,10 @@
     
     <div class="row">
     
-    <div class="col-md-12" role="main" id="main"><h1 id="Common_Workflow_Language_Standards,_v1.3.0-dev1" class="section">Common Workflow Language Standards, v1.3.0-dev1 <a href="#Common_Workflow_Language_Standards,_v1.3.0-dev1">&sect;</a></h1><p>The <a href="http://www.commonwl.org/user_guide/">User Guide</a> provides a gentle
-introduction to writing CWL command line tools and workflows. Currently the CWL User Guide targets CWL v1.0 only.</p>
+    <div class="col-md-12" role="main" id="main"><h1 id="Common_Workflow_Language_Standards,_v1.3.0-dev1" class="section">Common Workflow Language Standards, v1.3.0-dev1 <a href="#Common_Workflow_Language_Standards,_v1.3.0-dev1">&sect;</a></h1><p>This is an un-official, non-ratified, development version of the future CWL v1.3
+standard. Any changes from v1.2 could be modified before final ratification.</p>
+<p>The <a href="http://www.commonwl.org/user_guide/">User Guide</a> provides a gentle
+introduction to writing CWL command line tools and workflows.</p>
 <p>The CWL <a href="CommandLineTool.html">Command Line Tool Description Standard</a>
 specifies the document schema and execution semantics for wrapping and
 executing command line tools.</p>
