Update docs

docs/index.md

@@ -28,6 +28,8 @@ Documentation of [Cloudgene 2](https://v2.cloudgene.io/)
 
 ## :octicons-package-16: Integrate Your Nextflow pipelines
 
+Integrate your analysis pipeline into Cloudgene by writing a simple configuration file.
+
 === ":material-file: cloudgene.yaml"
 
     ```yaml
@@ -54,54 +56,70 @@ Documentation of [Cloudgene 2](https://v2.cloudgene.io/)
           description: Output
           type: local-folder
     ```
+=== ":material-file: Web-Interface"
+    ![alt text](images/index/cg-fetchngs.png)
+=== ":material-file: Results"
+    ![alt text](images/index/cg-fetchngs-results.png)
 ---
 
+## :fontawesome-solid-share: Share your pipeline
+
+Share your application via HTTP, GitHub, or S3, and enable users to install it with a simple command.
+
+```bash
+cloudgene install lukfor/cg-fetchngs
+```
+
 ## :fontawesome-solid-diagram-project: Combine Your Nextflow pipeline with others
 
+Combine your Nextflow pipeline with other pipelines and create use-case specific web services.
+
 === ":material-file: cloudgene.yaml"
 
     ```yaml
-    id: fetch-ngs
-    name: FetchNGS
-    description: Pipeline to fetch metadata and raw FastQ files from public databases
-    version: 1.12.0
-    website: https://github.com/nf-core/fetchngs
-    author: Harshil Patel, Moritz E. Beber and Jose Espinosa-Carrasco
+    id: taxprofiler
+    name: Taxprofiler
+    description: Taxonomic classification and profiling of shotgun short- and long-read metagenomic data
+    version: 1.1.8
+    website: https://github.com/nf-core/taxprofiler
+    author: James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, and the nf-core/taxprofiler team
     logo: https://raw.githubusercontent.com/nf-core/fetchngs/master/docs/images/nf-core-fetchngs_logo_light.png
-    
+
     workflow:
-    steps:
-      - name: Fetch Data
-        type: nextflow #set default?
-        script: nf-core/fetchngs
-        revision: 1.12.0
-        stdout: true # set deafault?
-        params:
-          input: "${input_ids}"
-
-      - name: Run Kraken2 using taxprofiler
-        type: nextflow #set default?
-        script: nf-core/taxprofiler
-        revision: 1.1.8
-        stdout: true # set deafault?
-        params:
-          input: "${outdir}/samplesheet/samplesheet.csv"
-          run_kraken2: true
-          databases: "https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_full_v1.2.csv"
-     
-    inputs:
-      - id: input_ids
-        description: IDs
-        type: textarea
-        writeFile: "ids.csv"
-        serialize: false
-
-    outputs:
-      - id: outdir
-        description: Output
-        type: local-folder
-    ```
+      steps:
+        - name: Fetch Data
+          script: nf-core/fetchngs
+          revision: 1.12.0
+          stdout: true
+          params:
+            input: "${input_ids}"
+
+        - name: Run taxprofiler
+          script: nf-core/taxprofiler
+          revision: 1.1.8
+          stdout: true
+          params:
+            input: "${outdir}/samplesheet/samplesheet.csv"
+            databases: "https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_full_v1.2.csv"
+            multiqc_title: "${CLOUDGENE_JOB_NAME}"
+
+      inputs:
+        - id: input_ids
+          description: IDs
+          type: textarea
+          value: "SRR12696236"
+          writeFile: "ids.csv"
+          serialize: false
 
+      outputs:
+        - id: outdir
+          description: Output
+          type: local_folder
+    ```
+=== ":material-file: Web-Interface"
+    ![alt text](images/index/cg-taxprofiler.png)
+=== ":material-file: Results"
+    ![alt text](images/index/cg-taxprofiler-results.png)
 ## Who uses Cloudgene?
 
 

docs/server/getting-started.md

@@ -1,21 +1,20 @@
-# Getting started
+# Getting Started
 
-This guide helps you to start Cloudgene and to install your first application. You have to install Cloudgene properly on your computer before you can start.
+This guide will help you start Cloudgene and install your first application. You must install Cloudgene properly on your computer before you can begin.
 
-## Start Cloudgene Server
+## Start the Cloudgene Server
 
-The webserver can be started with the following command:
+The web server can be started with the following command:
 
 ```sh
 ./cloudgene server
 ```
 
-The webservice is available on [http://localhost:8082](http://localhost:8082). Please use username `admin` and password `admin1978` to login. 
-The default port can be changed in the [configuration file](configuration.md#web-application).
+The web service is available at [http://localhost:8082](http://localhost:8082). Please use the username `admin` and password `admin1978` to log in. The default port can be changed in the [configuration file](configuration.md#web-application).
 
-## Install your first application
+## Install Your First Application
 
-Stop the webservice by pressing `CTRL-C`. The **cg-fetchngs** application can be installed by using the following command:
+Stop the web service by pressing `CTRL-C`. The **cg-fetchngs** application can be installed using the following command:
 
 ```sh
 ./cloudgene install lukfor/cg-fetchngs
@@ -27,21 +26,16 @@ Next, restart Cloudgene with the following command:
 ./cloudgene server
 ```
 
-Open Cloudgene in your browser and login. A new menu item **Run** appears in the menubar. Click on it to start a new job:
+Open Cloudgene in your browser and log in. A new menu item, **Run**, will appear in the menu bar. Click on it to start a new job:
 
-<div class="screenshot">
-<img src="../../images/screenshots/menubar.png">
-<img src="../../images/screenshots/hello-cloudgene.png">
-</div>
+![](../images/index/cg-fetchngs.png)
 
-The **hello-cloudgene** application displays several inspiring quotes:
+The **cg-fetchngs** application starts the nf-core pipeline, downloads the entered IDs, and provides the results for download.
 
-<div class="screenshot">
-<img src="../../images/screenshots/hello-cloudgene-results.png">
-</div>
+![](../images/index/cg-fetchngs-results.png)
 
-## What's next?
+## What's Next?
 
 - [Install additional applications](/server/install-apps)
-- [Configure and customize Cloudgene](/server/configuration) to support E-Mail notification, SSL cerificates,
-- Learn how to [manage permissions](/server/permissions) and [handle jobs](/daemon/jobs)
+- [Configure and customize Cloudgene](/server/configuration) to support email notifications and SSL certificates.
+- Learn how to [manage permissions](/server/permissions) and [handle jobs](/daemon/jobs).