CWL - Revision history

Axec@dote.ru at 11:22, 4 February 2022

2022-02-04T11:22:46Z

Axec@dote.ru at 08:45, 4 February 2022

2022-02-04T08:45:40Z

Axec@dote.ru at 07:51, 4 February 2022

2022-02-04T07:51:43Z

Axec@dote.ru at 07:49, 4 February 2022

2022-02-04T07:49:11Z

Axec@dote.ru at 07:46, 4 February 2022

2022-02-04T07:46:25Z

Axec@dote.ru at 07:45, 4 February 2022

2022-02-04T07:45:12Z

Axec@dote.ru at 07:44, 4 February 2022

2022-02-04T07:44:56Z

Axec@dote.ru at 07:36, 4 February 2022

2022-02-04T07:36:57Z

Axec@dote.ru: Created page with "The Common Workflow Language (CWL)Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, B..."

2022-02-04T07:35:20Z

Created page with "The Common Workflow Language (CWL)<ref>Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, B..."

New page

The Common Workflow Language (CWL)<ref>Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilović, Carole Goble, The CWL Community (2021):Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language.Communication of the ACM. https://doi.org/10.1145/3486897 Retrieved from arXiv 2105.07028 {{doi|https://arxiv.org/abs/2105.07028}}</ref> is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments [https://www.commonwl.org/ (CWL website)].
[[File:guyton.png|thumb|Overall Circulation model]]
[[File:guyton.png|thumb|Overall Circulation model]]

Standard describes execution of Command Line Tools including setting of arguments, environment requirements and conditions (e.g. execution in docker or remote server).
It also describes workflow scenarios combining several tools through their inputs and outputs.

Currently BioUML supports next features:

<ul>
<li>Import\export CWL command line tools and workflows. (fig. 1)</li>
<li>Representing of CWL files as analysis methods within BioUML interface (fig. 2).</li>
<li>Visual representation of CWL workflows as visual diagrams (fig. 3).
<li>Setting of parameters and execution of CWL worklfows and tools. Execution is performed with cwl-runner tool. Produced result is stored in BioUML repository. (fig.4)</li>
</ul>

Currently there are several limitations in CWL support which we plan to overcome in future:
<ul>
<li>CWL tools may be imported only in designated folder within BioUMl interface. (Workflows can be imported anywhere)</li>
<li>Only workflows referencing separate cwl files as their steps can be imported</li>
<li>Referenced cwl files should be preliminary imported before the workflow</li>
<li>Visual diagram is used only for representation of CWL scenario and can not be edited</li>
<li>Started execution of CWL scenario or tool can not be stopped manually until it is finished</li>
</ul>

==== References ====
<references/>

@@ Line 1: / Line 1: @@
-[[File:cwl_import.png|thumb|Fig. 1. CWL import]]
+[[File:cwl_document.png|thumb|Fig. 1. CWL document]]
-[[File:cwl_analysis.png|thumb|Fig. 2. CWL analysis]]
+[[File:cwl_import.png|thumb|Fig. 2. CWL import]]
-[[File:cwl_workflow.png|thumb|Fig. 3. CWL workflow]]
+[[File:cwl_analysis.png|thumb|Fig. 3. CWL analysis]]
-[[File:cwl_execution.png|thumb|Fig. 4. CWL execution]]
+[[File:cwl_workflow.png|thumb|Fig. 4. CWL workflow]]
 The Common Workflow Language (CWL)<ref>Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilović, Carole Goble, The CWL Community (2021):Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language.Communication of the ACM. https://doi.org/10.1145/3486897 Retrieved from arXiv 2105.07028 {{doi|https://arxiv.org/abs/2105.07028}}</ref> is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments [https://www.commonwl.org/ (CWL website)].
@@ Line 8: / Line 9: @@
 Standard describes execution of Command Line Tools including setting of arguments, environment requirements and conditions (e.g. execution in docker or remote server).
 It also describes workflow scenarios combining several tools through their inputs and outputs.
 Currently BioUML supports next features:
 <ul>
-<li>Import of CWL command line tools and workflows. Representing them as data elements in BioUML repository (fig. 1).</li>
+<li>Import of CWL command line tools and workflows. Representing them as data elements in BioUML repository (fig. 2).</li>
-<li>Representing of CWL files as analysis methods  within BioUML interface (fig. 2).</li>
+<li>Representing of CWL files as analysis methods  within BioUML interface (fig. 3).</li>
-<li>Visual representation of CWL workflows as visual diagrams (fig. 3).
+<li>Visual representation of CWL workflows as visual diagrams (fig. 4).
-<li>Setting of parameters and execution of CWL worklfows and tools. Produced result is stored in BioUML repository (fig.4).</li>
+<li>Setting of parameters and execution of CWL worklfows and tools. Produced result is stored in BioUML repository (fig.5).</li>
 <li>Execution is performed with reference implementation of CWL - cwltool, thus we support all features supported by it.</li>
 </ul>

@@ Line 1: / Line 1: @@
-[[File:cwl_import.png|thumb|CWL import]]
+[[File:cwl_import.png|thumb|Fig. 1. CWL import]]
-[[File:cwl_analysis.png|thumb|CWL analysis]]
+[[File:cwl_analysis.png|thumb|Fig. 2. CWL analysis]]
-[[File:cwl_workflow.png|thumb|CWL workflow]]
+[[File:cwl_workflow.png|thumb|Fig. 3. CWL workflow]]
-[[File:cwl_execution.png|thumb|CWL execution]]
+[[File:cwl_execution.png|thumb|Fig. 4. CWL execution]]
 The Common Workflow Language (CWL)<ref>Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilović, Carole Goble, The CWL Community (2021):Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language.Communication of the ACM. https://doi.org/10.1145/3486897 Retrieved from arXiv 2105.07028 {{doi|https://arxiv.org/abs/2105.07028}}</ref> is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments [https://www.commonwl.org/ (CWL website)].

@@ Line 12: / Line 12: @@
 <ul>
-<li>Import\export CWL command line tools and workflows. Representing them as data elements in BioUML repository (fig. 1).</li>
+<li>Import of CWL command line tools and workflows. Representing them as data elements in BioUML repository (fig. 1).</li>
 <li>Representing of CWL files as analysis methods  within BioUML interface (fig. 2).</li>
 <li>Visual representation of CWL workflows as visual diagrams (fig. 3).

@@ Line 15: / Line 15: @@
 <li>Representing of CWL files as analysis methods  within BioUML interface (fig. 2).</li>
 <li>Visual representation of CWL workflows as visual diagrams (fig. 3).
-<li>Setting of parameters and execution of CWL worklfows and tools. Execution is performed with cwl-runner tool. Produced result is stored in BioUML repository (fig.4).</li>
+<li>Setting of parameters and execution of CWL worklfows and tools. Produced result is stored in BioUML repository (fig.4).</li>
 </ul>
@@ Line 24: / Line 25: @@
 <li>Referenced cwl files should be preliminary imported before the workflow</li>
 <li>Visual diagram is used only for representation of CWL scenario and can not be edited</li>
-<li>BioUML workflows supports only files outputs and inputs. Strings, numerica and boolean values are not represented in visualisation</li>
+<li>BioUML workflows supports only files outputs and inputs. Strings, numerical and boolean values are not represented in visualisation</li>
 <li>Started execution of CWL scenario or tool can not be stopped manually until it is finished</li>
 </ul>