Basic documentation of CWL export feature (#232)

.github/CONTRIBUTING.md

@@ -72,4 +72,4 @@ Thank you for your contribution!
 Finally, please add your name below:
 
 1. OpenMS Team
-
+2. Michael R. Crusoe

CHANGELOG.md

@@ -3,11 +3,10 @@
 ------------------------------------------------------------------------------------------
 
  - fix some TOPPAS inaccuracies
-
-
+ - Added CWL to the list of supported workflow languages
 
 ------------------------------------------------------------------------------------------
 ----                                OpenMS 3.0     (released 7/2023)                  ----
 ------------------------------------------------------------------------------------------
 
- - initial version
+ - initial version

docs/about/installation.rst

@@ -15,7 +15,7 @@ You can run OpenMS TOPP tools from the command line using your custom scripts, o
 workflow systems designed to make workflow creation and maintenance more fun, find out more in :ref:`workflows`.
 
 .. list-table::
-   :widths: 25 25 25 25
+   :widths: 20 20 20 20 20
    :class: borderless only-light
    :align: center
 
@@ -35,9 +35,13 @@ workflow systems designed to make workflow creation and maintenance more fun, fi
          :target: ../getting-started/toppas-get-started.html
          :width: 90%
 
+     - .. image:: /_images/introduction/CWL-4K.png
+         :target: ../getting-started/cwl-get-started.html
+         :width: 90%
+
 
 .. list-table::
-   :widths: 25 25 25 25
+   :widths: 20 20 20 20 20
    :class: borderless only-dark
    :align: center
 
@@ -57,6 +61,9 @@ workflow systems designed to make workflow creation and maintenance more fun, fi
          :target: ../getting-started/toppas-get-started.html
          :width: 90%
 
+     - .. image:: /_images/introduction/CWL-4K.png
+         :target: ../getting-started/cwl-get-started.html
+         :width: 90%
 
 Graphical and Command-Line Tools
 --------------------------------

docs/getting-started/cwl-get-started.md

@@ -0,0 +1,10 @@
+Common Workflow Language
+========================
+
+The Common Workflow Language is a set of free and open standards for describing
+command-line tool and workflows made from those tool descriptions.
+
+Every OpenMS tool from version 3.2 onwards can self-generate a CWL tool description
+using the `-write_cwl` option.
+
+For example: `PeakPickerHiRes -write_cwl PeakPickerHiRes.cwl`

docs/getting-started/workflows.rst

@@ -101,6 +101,25 @@ workflow systems designed to make workflow creation and maintenance more fun:
 
         OpenMS' build-in workflow system, with limited capabilities but easy to use and tailored to TOPP tools.
 
+    .. grid-item-card:: CWL
+        :img-top: /_images/introduction/CWL-4K.png
+        :link: /getting-started/cwl-get-started
+        :link-type: doc
+        :class-card: only-light
+        :class-img-top: halfwidth
+        :columns: 12
+
+        The Common Workflow Language standards are automatically supported by every OpenMS tool from version 3.2 and onwards.
+
+    .. grid-item-card:: CWL
+        :img-top: /_images/introduction/CWL-4K.png
+        :link: /getting-started/cwl-get-started
+        :link-type: doc
+        :class-card: only-dark
+        :class-img-top: halfwidth
+        :columns: 12
+
+        The Common Workflow Language standards are automatically supported by every OpenMS tool from version 3.2 and onwards.
 
 .. toctree::
     :maxdepth: 1
@@ -109,4 +128,5 @@ workflow systems designed to make workflow creation and maintenance more fun:
     /getting-started/knime-get-started.md
     /getting-started/nextflow-get-started.md
     /getting-started/galaxy-get-started.md
-    /getting-started/toppas-get-started.md
+    /getting-started/toppas-get-started.md
+    /getting-started/cwl-get-started.md