GitPod base image: Always self-update to the latest version of Nextflow.

.gitpod.yml

@@ -5,6 +5,7 @@ tasks:
       python -m pip install -e .
       python -m pip install -r requirements-dev.txt
       pre-commit install --install-hooks
+      nextflow self-update
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

CHANGELOG.md

@@ -14,6 +14,9 @@
 
 ### General
 
+- GitPod base image: Always self-update to the latest version of Nextflow. Add [pre-commit](https://pre-commit.com/) dependency.
+- GitPod configs: Update Nextflow as an init task, init pre-commit in pipeline config.
+
 # [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27]
 
 ### Template

nf_core/gitpod/gitpod.Dockerfile

@@ -38,13 +38,17 @@ RUN conda config --add channels defaults && \
     conda config --set channel_priority strict && \
     conda install --quiet --yes --name base mamba && \
     mamba install --quiet --yes --name base \
-    nextflow=22.10.1 \
-    nf-core \
-    nf-test \
-    black \
-    prettier \
-    pytest-workflow && \
+        nextflow \
+        nf-core \
+        nf-test \
+        black \
+        prettier \
+        pre-commit \
+        pytest-workflow && \
     mamba clean --all -f -y
 
+# Update Nextflow
+RUN nextflow self-update
+
 # Install nf-core
 RUN python -m pip install .

nf_core/pipeline-template/.gitpod.yml

@@ -1,4 +1,9 @@
 image: nfcore/gitpod:latest
+tasks:
+  - name: Update Nextflow and setup pre-commit
+    command: |
+      pre-commit install --install-hooks
+      nextflow self-update
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack