Merge pull request #522 from nfdi4plants/cwl

reorder cwl articles

src/content/docs/cwl/cwl-examples.md

@@ -3,6 +3,8 @@ title: "CWL Examples"
 lastUpdated: 2024-02-05
 authors:
   - caro-ott
+sidebar:
+  order: 4
 ---
 
 # CWL Examples

src/content/docs/cwl/cwl-introduction.md

@@ -3,11 +3,13 @@ title: "CWL Introduction"
 lastUpdated: 2024-01-18
 authors:
   - caro-ott
+sidebar:
+  order: 1
 ---
 
 # What is CWL?
 
-CWL is short for Common Workflow Language.
+CWL is short for **Common Workflow Language**.
 It is an open standard for describing how to run command line tools and connect them to create 
 workflows, which can then be incorporated in other workflows if needed (nested workflows). 
 Descriptions in CWL are portable across a variety of platforms that support the CWL 

src/content/docs/cwl/cwl-metadata.md

@@ -3,6 +3,8 @@ title: "CWL Metadata"
 lastUpdated: 2024-02-05
 authors:
   - caro-ott
+sidebar:
+  order: 3
 ---
 
 # CWL Metadata

src/content/docs/cwl/cwl-runner-installation.mdx

@@ -0,0 +1,78 @@
+---
+title: "CWL Runner Installation"
+lastUpdated: 2024-01-18
+authors:
+  - caro-ott
+sidebar:
+  order: 2
+---
+
+The recommended CWL runner is [cwltool](https://github.com/common-workflow-language/cwltool), the reference implementation for the CWL standards.
+
+import { Steps } from '@astrojs/starlight/components';
+import { Tabs, TabItem } from '@astrojs/starlight/components';
+
+
+<Tabs syncKey="os">
+<TabItem label="Windows" icon='seti:windows'>
+
+The installation on Windows can be done following the guide [here](https://cwltool.readthedocs.io/en/latest/#ms-windows-users).
+
+<Steps>
+
+1. Install Windows Subsystem for Linux from the Microsoft Store
+
+    ![WSL](@images/guides/cwl/wsl.png)
+
+2. Install Debian from the Microsoft Store
+
+    ![Debian](@images/guides/cwl/debian.png)
+
+3. Set Debian as your default WSL 2 distro: `wsl --set-default debian`
+4. Install [Docker Desktop for Windows](https://desktop.docker.com/win/main/amd64/Docker%20Desktop%20Installer.exe)
+   - Start Docker Desktop and Navigate to Settings
+   - Select "Use WSL 2 based engine" in the general tab and apply
+      ![Docker WSL2](@images/guides/cwl/docker-wsl2.png)
+   - Select "Enable Integration with my default distro" in the resources tab under WSL Integration
+      ![Docker WSL Integration](@images/guides/cwl/docker-wsl-integration.png)
+5. Start WSL
+6. Follow the Instructions for Linux (Debian/Ubuntu)
+
+</Steps>
+</TabItem>
+
+{/* <TabItem label="Macos" icon="apple">
+<Steps>
+</Steps>
+</TabItem> */}
+
+<TabItem label="Linux" icon='linux'>
+
+For installation on Linux (Debian/Ubuntu): 
+
+<Steps>
+
+1. Run `sudo apt-get update`
+2. Install Python 3 if it is not already preinstalled `sudo apt install python3`
+3. Install python virtual environment `sudo apt install python3.[your version here]-venv`
+4. Create a virtual environment `python3 -m venv env` (named env here, name can vary)
+5. Activate the virtual environment `source env/bin/activate`
+6. Install `cwltool` with pip `pip install cwltool`
+
+</Steps>
+
+</TabItem>
+
+</Tabs>
+
+
+## cwltool usage
+
+- If you are on Windows, start the WSL
+- Activate the virtual environment `source env/bin/activate`
+- Navigate to the results destination directory
+- Run `cwltool` by specifying the CWL `Workflow` or `CommandLineTool` description file path and the (optional) inputs file path (you can use relative or full paths): 
+
+```bash
+cwltool path/to/cwlfile.cwl path/to/jobfile.yml
+```

src/content/docs/cwl/index.mdx

@@ -3,6 +3,8 @@ title: Computational Workflows
 lastUpdated: 2023-02-05
 authors:
   - kevin-frey
+sidebar:
+  order: 0
 ---
 import { CardGrid } from '@astrojs/starlight/components';
 import { LinkCard } from '@astrojs/starlight/components';