Cleaned up some missed mentions. Removed some old screenshot images

Author: ewels

docs/basic_training/containers.md

@@ -126,7 +126,7 @@ docker images
 
     ??? Solution
 
-        Use your favorite editor (e.g., `vim` or `nano`) to create a file named `Dockerfile`. Alternatively, run `code Dockerfile` to create a a file named `Dockerfile` in Gitpod. Copy the following content:
+        Use your favorite editor (e.g., `vim` or `nano`) to create a file named `Dockerfile`. Alternatively, run `code Dockerfile` to create a a file named `Dockerfile`. Copy the following content:
 
         ```dockerfile linenums="1" title="Dockerfile"
         FROM debian:bullseye-slim
@@ -624,7 +624,7 @@ mulled-search --destination quay singularity --channel bioconda --search bowtie
 
 !!! question "Exercise"
 
-    During the earlier RNA-Seq tutorial (script2.nf), you created an index with the salmon tool. Given you do not have salmon installed locally in the machine provided by Gitpod, you had to either run it with `-with-conda` or `-with-docker`. Your task now is to run it again `-with-docker`, but without creating your own container image. Instead, use the BioContainers image for salmon 1.7.0.
+    During the earlier RNA-Seq tutorial (script2.nf), you created an index with the salmon tool. Given you do not have salmon installed locally in the machine provided by GitHub Codespaces, you had to either run it with `-with-conda` or `-with-docker`. Your task now is to run it again `-with-docker`, but without creating your own container image. Instead, use the BioContainers image for salmon 1.7.0.
 
 
     ??? Solution

docs/basic_training/img/gitpod.welcome.png

@@ -1,16 +1,16 @@
 # Orientation
 
-The Gitpod environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself.
+The GitHub Codespaces environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself.
 However, you do need a (free) account to log in, and you should take a few minutes to familiarize yourself with the interface.
 
 If you have not yet done so, please follow [this link](../../envsetup/) before going any further.
 
 ## Materials provided
 
-Throughout this training course, we'll be working in the `hello-nextflow/` directory, which loads by default when you open the Gitpod workspace.
+Throughout this training course, we'll be working in the `hello-nextflow/` directory, which loads by default when you open the GitHub Codespaces workspace.
 This directory contains all the code files, test data and accessory files you will need.
 
-Feel free to explore the contents of this directory; the easiest way to do so is to use the file explorer on the left-hand side of the Gitpod workspace.
+Feel free to explore the contents of this directory; the easiest way to do so is to use the file explorer on the left-hand side of the GitHub Codespaces workspace.
 Alternatively, you can use the `tree` command.
 Throughout the course, we use the output of `tree` to represent directory structure and contents in a readable form, sometimes with minor modifications for clarity.
 

docs/hello_nextflow/01_orientation.md

@@ -36,7 +36,7 @@ cat output.txt
 
 !!! tip
 
-    In the Gitpod environment, you can also find the output file in the file explorer, and view its contents by clicking on it. Alternatively, you can use the `code` command to open the file for viewing.
+    In the GitHub Codespaces environment, you can also find the output file in the file explorer, and view its contents by clicking on it. Alternatively, you can use the `code` command to open the file for viewing.
 
     ```bash
     code output.txt
@@ -181,7 +181,7 @@ Have a look inside; you'll find a subdirectory named with a hash (in order to ma
 
 !!! tip
 
-    If you browse the contents of the task subdirectory in the Gitpod's VSCode file explorer, you'll see all these files right away.
+    If you browse the contents of the task subdirectory in the VSCode file explorer, you'll see all these files right away.
     However, these files are set to be invisible in the terminal, so if you want to use `ls` or `tree` to view them, you'll need to set the relevant option for displaying invisible files.
 
     ```bash

docs/hello_nextflow/02_hello_world.md

@@ -131,7 +131,7 @@ gatk HaplotypeCaller \
         -L /data/ref/intervals.bed
 ```
 
-The output file `reads_mother.vcf` is created inside your working directory in the container, so you won't see it in the Gitpod file explorer unless you change the output file path.
+The output file `reads_mother.vcf` is created inside your working directory in the container, so you won't see it in the VS Code file explorer unless you change the output file path.
 However, it's a small test file, so you can `cat` it to open it and view the contents.
 If you scroll all the way up to the start of the file, you'll find a header composed of many lines of metadata, followed by a list of variant calls, one per line.
 
@@ -732,7 +732,7 @@ As you can see, we listed one file path per line, and they are absolute paths.
 
 !!! note
 
-    The files we are using here are just on your Gitpod's local filesystem, but we could also point to files in cloud storage.
+    The files we are using here are just on your GitHub Codespaces's local filesystem, but we could also point to files in cloud storage.
 
 ### 4.2. Update the parameter default
 

docs/hello_nextflow/04_hello_genomics.md

@@ -468,7 +468,7 @@ Basically we are telling Nextflow to generate a Slurm submission script and subm
 
 ### 3.2. Launch the workflow to generate the job submission script
 
-Let's try running this; even though we know it won't execute (since we don't have Slurm set up in this Gitpod environment) we'll be able to see what the submission script looks like.
+Let's try running this; even though we know it won't execute (since we don't have Slurm set up in this GitHub Codespaces environment) we'll be able to see what the submission script looks like.
 
 ```bash
 nextflow run main.nf -profile conda_on
@@ -720,7 +720,7 @@ To have Nextflow generate the report automatically, simply add `-with-report <fi
 nextflow run main.nf -profile my_laptop -with-report report-config-1.html
 ```
 
-The report is an html file, which you can download and open in your browser. You can also right click it in the file explorer on the left and click on `Show preview` in order to view it on Gitpod.
+The report is an html file, which you can download and open in your browser. You can also right click it in the file explorer on the left and click on `Show preview` in order to view it in GitHub Codespaces.
 
 Take a few minutes to look through the report and see if you can identify some opportunities for adjusting resources.
 Make sure to click on the tabs that show the utilization results as a percentage of what was allocated.
@@ -829,7 +829,7 @@ _After:_
     }
 ```
 
-We can't test this since we don't have a live connection to Slurm in the Gitpod environment.
+We can't test this since we don't have a live connection to Slurm in the GitHub Codespaces environment.
 However, you can try running the workflow with resource allocations that exceed these limits, then look up the `sbatch` command in the `.command.run` script file.
 You should see that the requests that actually get sent to the executor are capped at the values specified by `resourceLimits`.
 

docs/hello_nextflow/06_hello_config.md

@@ -43,7 +43,7 @@ When you're ready to get down to work, click on the 'Open in GitHub Codespaces'
 
         :material-lightbulb: Essential for setting up your environment for the first time.
 
-    Instructions for setting up your environment to work through training materials (all courses). Provides an orientation to Gitpod as well as alternate installation instructions for working on your own local machine.
+    Instructions for setting up your environment to work through training materials (all courses). Provides an orientation to GitHub Codespaces as well as alternate installation instructions for working on your own local machine.
 
     [Launch the Environment Setup training :material-arrow-right:](envsetup/index.md){ .md-button .md-button--primary }
 
@@ -121,7 +121,7 @@ When you're ready to get down to work, click on the 'Open in GitHub Codespaces'
 
         :material-run-fast: A short hands-on tutorial focused on a concrete analysis pipeline example.
 
-    This course was developed as a "learn by doing" tutorial intended as a fast, hands-on way to get to grips with Nextflow using a very concrete analysis pipeline example. You can still find the materials in the GitHub repository, but it is no longer being maintained and can no longer be launched in Gitpod or in the training portal.
+    This course was developed as a "learn by doing" tutorial intended as a fast, hands-on way to get to grips with Nextflow using a very concrete analysis pipeline example. You can still find the materials in the GitHub repository, but it is no longer being maintained and can no longer be launched in GitHub Codespaces or in the training portal.
 
 ## Resources
 

docs/index.md

@@ -20,34 +20,6 @@ This is an empty directory where you will create an launch your pipeline.
     cd /workspace/gitpod/nf-develop
     ```
 
-<!---
-
-## Configuring GitHub
-
-As a part of this workshop you will push changes to your GitHub.
-
-If this is the first time you have used Gitpod for development work you will need to edit your permissions to push changes.
-
-To edit your Gitpod permissions, open your Gitpod dashboard by clicking on the three horizontal lines in the top left-hand corner of your browser window and select `Gitpod: Open Dashboard` from the dropdown menu.
-
-![Open Gitpod dashboard](img/gitpod.opendashboard.png)
-
-In your dashboard, click on your avatar in the top right-hand corner of your window and select `User Settings` from the dropdown menu.
-
-![Gitpod dashboard](img/gitpod.dashboard.png)
-
-Click on `Git Providers` on the right hand menu.
-
-![Git providers](img/gitpod.providers.png)
-
-Edit the permissions for your GitHub account by clicking on the three dots next to your GitHub account and give your Gitpod account permissions to access for GitHub repositories.
-
-![GitHub permissions](img/gitpod.permissions.png)
-
-Once complete, click `Update permissions` and return to your Gitpod training environment.
-
--->
-
 ---
 
 Congratulations! You are now ready to start the workshop!