nextflow-io · ewels · Feb 18, 2025 · Feb 18, 2025 · Feb 18, 2025 · Feb 18, 2025
diff --git a/.gitpod.yml b/.gitpod.yml
diff --git a/docs/envsetup/index.md b/docs/envsetup/index.md
@@ -9,3 +9,15 @@ If you already have a GitHub Codespaces account, click on the button below, othe
 Let's get started!
 
 [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
+
+For more detailed instructions for GitHub Codespaces, see the [GitHub Codespaces env-setup docs](01_setup.md).
+If you cannot use GitHub Codespaces and wish to use a local development environment, see the [documentation for local installation](02_local.md).
+
+!!! info "Deprecation of GitPod"
+
+    Nextflow Training used to use [Gitpod](https://gitpod.io) until February 2025.
+    However, the makers of Gitpod have decided to retire the free functionality in favor of their new [Gitpod Flex](https://www.gitpod.io/blog/introducing-gitpod-flex) system.
+    For that reason, we have switched to using GitHub Codespaces, which also offer a one-click developer environment with no prior setup.
+
+    Depending on when you signed up to GitPod and when exactly they retire the service, you may still be able to launch the training in their old cloud IDE, though we cannot guarantee reliable access going forward:
+    [Open in Gitpod](https://gitpod.io/#https://github.com/nextflow-io/training).
diff --git a/docs/index.md b/docs/index.md
@@ -22,20 +22,11 @@ When you're ready to get down to work, click on the 'Open in GitHub Codespaces'
 
 [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
 
-!!! note
-
-    Nextflow Training used to use [Gitpod](https://gitpod.io) until February 2025.
-    However, the makers of Gitpod have decided to retire the free functionality in favor of their new [Gitpod Flex](https://www.gitpod.io/blog/introducing-gitpod-flex) system.
-    For that reason, we have switched to using GitHub Codespaces, which also offer a one-click developer environment with no prior setup.
-
-    Depending on when you signed up to GitPod and when exactly they retire the service, you may still be able to launch the training in their old cloud IDE, though we cannot guarantee reliable access going forward:
-    [Open in Gitpod](https://gitpod.io/#https://github.com/nextflow-io/training).
-
 ## Training Environment Setup
 
 !!! exercise "Environment Setup"
 
-    !!! quote inline end ""
+    !!! tip inline end ""
 
         :material-lightbulb: Set up your environment for the first time.
 
@@ -49,20 +40,22 @@ These are foundational, domain-agnostic courses intended for those who are compl
 
 !!! exercise "Hello Nextflow"
 
-    !!! quote inline end ""
+    !!! tip inline end ""
 
         :material-run-fast: Learn to develop pipelines in Nextflow.
 
     This is a course for newcomers who wish to learn how to develop their own pipelines. The course covers the core components of the Nextflow language in enough detail to enable developing simple but fully functional pipelines. It also covers key elements of pipeline design, development and configuration practices.
 
     [Launch the Hello Nextflow training :material-arrow-right:](hello_nextflow/index.md){ .md-button .md-button--primary }
 
-**Coming soon:** "Nextflow Run" — Learn to run Nextflow pipelines (run only, no code development)
+!!! info ""
+
+    **Coming soon:** "Nextflow Run" — Learn to run Nextflow pipelines (run only, no code development)
 
 <!-- COMMENTED OUT UNTIL THIS IS READY
 !!! exercise "Nextflow Run"
 
-    !!! quote inline end ""
+    !!! tip inline end ""
 
         :material-run-fast: Learn to run Nextflow pipelines.
 
@@ -77,20 +70,22 @@ These are courses that demonstrate how to apply the concepts and components pres
 
 !!! exercise "Nextflow for Genomics"
 
-    !!! quote inline end ""
+    !!! tip inline end ""
 
         :material-run-fast: Learn to develop a pipeline for genomics in Nextflow.
 
     This is a course for researchers who wish to learn how to develop their own genomics pipelines. The course uses a variant calling use case to demonstrate how to develop a simple but functional genomics pipeline.
 
     [Launch the Nextflow for Genomics training :material-arrow-right:](nf4_science/genomics/){ .md-button .md-button--primary }
 
-**Coming soon:** "Nextflow for RNAseq" — Learn to develop a pipeline for bulk RNAseq analysis in Nextflow
+!!! info ""
+
+    **Coming soon:** "Nextflow for RNAseq" — Learn to develop a pipeline for bulk RNAseq analysis in Nextflow
 
 <!-- COMMENTED OUT UNTIL THIS IS READY
 !!! exercise "Nextflow for RNAseq"
 
-    !!! quote inline end ""
+    !!! tip inline end ""
 
         :material-run-fast: Learn to develop a pipeline for bulk RNAseq analysis in Nextflow.
 
@@ -106,7 +101,7 @@ These are courses that demonstrate how to use Nextflow features in more detail o
 <!-- COMMENTED OUT UNTIL THE FIRST ONE IS READY
 !!! exercise "Side Quests"
 
-    !!! quote inline end ""
+    !!! tip inline end ""
 
         :material-run-fast: Training modules for a variety of topics of interest.
 
@@ -117,7 +112,7 @@ These are courses that demonstrate how to use Nextflow features in more detail o
 
 !!! exercise "Fundamentals Training"
 
-    !!! tip inline end ""
+    !!! quote inline end ""
 
         :material-lightbulb: Comprehensive training material for exploring the full scope of Nextflow's capabilities.
 

diff --git a/docs/nextflow_run/01_orientation.md b/docs/nextflow_run/01_orientation.md
@@ -40,7 +40,7 @@ If you run this inside `run-nextflow`, you should see the following output: [TOD
     If for whatever reason you move out of this directory, you can always run this command to return to it:
 
     ```bash
-    cd /workspace/gitpod/run-nextflow
+    cd /workspaces/training/run-nextflow
     ```
 
 Now, to begin the course, click on the arrow in the bottom right corner of this page.
diff --git a/docs/nf4_science/genomics/00_orientation.md b/docs/nf4_science/genomics/00_orientation.md
@@ -65,7 +65,7 @@ _Completed workflows (solutions) will be added in the near future._
     If for whatever reason you move out of this directory, you can always run this command to return to it:
 
     ```bash
-    cd /workspace/gitpod/nf4-science/genomics
+    cd /workspaces/training/nf4-science/genomics
     ```
 
 Now, to begin the course, click on the arrow in the bottom right corner of this page.
diff --git a/docs/side_quests/orientation.md b/docs/side_quests/orientation.md
@@ -40,7 +40,7 @@ If you run this inside `tapas`, you should see the following output: [TODO]
     If for whatever reason you move out of this directory, you can always run this command to return to it:
 
     ```bash
-    cd /workspace/gitpod/tapas
+    cd /workspaces/training/tapas
     ```
 
 Now, to begin the course, click on the arrow in the bottom right corner of this page.
diff --git a/gitpod-ws.code-workspace b/gitpod-ws.code-workspace