Merge remote-tracking branch 'matteo/develop' into develop

# Conflicts:
#	docs/about/installation.rst
#	docs/getting-started/introduction.rst
#	docs/getting-started/workflows.rst
#	docs/manual/develop.md
#	docs/tutorials/knime-user-tutorial.md

.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

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,7 +15,7 @@ PRs should be made against the development branch.
 ## PR checklist
 
 - [ ] I have added description of the change I'm proposing in the OpenMS Documentation.
-- [ ] I have read and followed [OpenMS Documentation Contributing guidelines](CONTRIBUTING.md).
+- [ ] I have read and followed [OpenMS Documentation Contributing guidelines](/.github/CONTRIBUTING.md).
 - [ ] I have attached a screenshot of the relevant area after this change.
 - [ ] `CHANGELOG.md` is updated.
-- [ ] I have added my name in [CONTRIBUTING.md](CONTRIBUTING.md#openms-documentation-contributors).
+- [ ] I have added my name in [CONTRIBUTING.md](/.github/CONTRIBUTING.md#openms-documentation-contributors).

CHANGELOG.md

@@ -1,13 +1,12 @@
 ------------------------------------------------------------------------------------------
-----                                OpenMS 3.1.0     (released: under development)    ----
+----                                OpenMS 3.2.0     (released: under development)    ----
 ------------------------------------------------------------------------------------------
 
  - 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/conf.py

@@ -26,12 +26,12 @@
 # built documents.
 #
 # The short major.minor.patch version.
-version = '3.1.0'
+version = '3.2.0'
 # Short version for the latest supported KNIME
 knime_version = '5.2.0'
 
 # The full version, including alpha/beta/rc tags.
-release = '3.1.0dev'
+release = '3.2.0'
 
 # -- General configuration ---------------------------------------------------
 

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/introduction.rst

@@ -60,7 +60,7 @@ Should you be missing something you can also add new functions or classes to the
             :margin: 0
 
             .. grid-item-card:: :material-regular:`account_tree;5em;sd-text-info` **Workflow Editor**
-                :link: /getting-started/webapps
+                :link: /getting-started/workflows
                 :link-type: doc
 
                 **Use a supported workflow editor to create or run predefined workflows.**

docs/getting-started/workflows.rst

@@ -93,14 +93,33 @@ workflow systems designed to make workflow creation and maintenance more fun:
 
     .. grid-item-card:: TOPPAS
         :img-top: /_images/introduction/TOPPAS_logo_dark.png
-        :link: /manual/develop
+        :link: /getting-started/toppas-get-started
         :link-type: doc
         :class-card: only-dark
         :class-img-top: halfwidth
         :columns: 12
 
         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

docs/manual/develop.md

@@ -3,8 +3,7 @@ Developers
 
 To contribute to OpenMS:
 
-- Familiarise yourself with the OpenMS online documentation.
-- Learn how to [build OpenMS](/about/installation.rst).
+- Familiarise yourself with the OpenMS technical documentation.
 - Check out the [OpenMS tutorial for developers](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/tutorial.html#tutorial_developing).
 
 For any questions, please [contact us](/about/communication.md).
@@ -82,4 +81,4 @@ develop/developer-guidelines-for-adding-new-dependent-libraries.md
 develop/link-external-code-to-openms.md
 develop/developer-faq.md
 
-```
+```

docs/tutorials-and-quickstart-guides/openms-user-tutorial.md

@@ -36,7 +36,7 @@ If you are working through this tutorial at home/online, proceed with the follow
   not conda, nor docker.
   :::
 
-- Download and install [KNIME](https://www.knime.org/downloads/overview)
+- Download and install [KNIME](https://www.knime.org/downloads/)
 
 ::::
 

docs/tutorials/knime-user-tutorial.md

@@ -42,7 +42,7 @@ If you are working through this tutorial at home/online, proceed with the follow
   not conda, nor docker.
   :::
 
-- Download and install [KNIME](https://www.knime.org/downloads/overview)
+- Download and install [KNIME](https://www.knime.org/downloads/)
 
 ::::