Skip to content

Commit 063d788

Browse files
committed
1 parent dbcc70f commit 063d788

23 files changed

+28
-26
lines changed

draft-3/CommandLineTool.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

draft-3/SchemaSalad.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

draft-3/Workflow.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

draft-3/index.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

features/index.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -182,7 +182,7 @@ <h2 id="parallelization-and-scale-with-cwl">
182182
is determined by the dependencies between steps. Workflow steps which do not
183183
depend on one another may run in parallel.</p>
184184

185-
<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>
185+
<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>
186186

187187
<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>
188188

getting-started/index.html

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -95,9 +95,9 @@ <h1 class="post-title col-lg-10">
9595
<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>
9696

9797
<ul>
98-
<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>
98+
<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>
9999
<li>Browse <a href="/implementations/">CWL Implementations</a> to find a software package that’s right for you.</li>
100-
<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>
100+
<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>
101101
<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>
102102
<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>
103103
<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>

tools/index.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -454,7 +454,7 @@ <h3 id="specs">
454454
</tr>
455455
<tr>
456456
<td><a href="https://edamontology.org/">EDAM</a></td>
457-
<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>
457+
<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>
458458
</tr>
459459
<tr>
460460
<td><a href="https://schema.org/">schema.org</a></td>

v1.0/CommandLineTool.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.0/SchemaSalad.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.0/Workflow.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.0/index.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.1/CommandLineTool.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.1/SchemaSalad.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.1/Workflow.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.1/index.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.2/CommandLineTool.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.2/SchemaSalad.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.2/Workflow.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.2/index.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.3/CommandLineTool.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.3/SchemaSalad.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.3/Workflow.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>

v1.3/index.html

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
88
<link rel="stylesheet" href="/assets/styles-fix.css" />
99
<link rel="shortcut icon"
10-
href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
10+
href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
1111
<link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
1212

1313
<script>
@@ -122,8 +122,10 @@
122122

123123
<div class="row">
124124

125-
<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
126-
introduction to writing CWL command line tools and workflows. Currently the CWL User Guide targets CWL v1.0 only.</p>
125+
<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
126+
standard. Any changes from v1.2 could be modified before final ratification.</p>
127+
<p>The <a href="http://www.commonwl.org/user_guide/">User Guide</a> provides a gentle
128+
introduction to writing CWL command line tools and workflows.</p>
127129
<p>The CWL <a href="CommandLineTool.html">Command Line Tool Description Standard</a>
128130
specifies the document schema and execution semantics for wrapping and
129131
executing command line tools.</p>

0 commit comments

Comments
 (0)