Update gitpod

.gitpod.yml

@@ -6,17 +6,14 @@ tasks:
       python -m pip install -r requirements-dev.txt
       pre-commit install --install-hooks
       nextflow self-update
-  - name: unset JAVA_TOOL_OPTIONS
-    command: |
-      unset JAVA_TOOL_OPTIONS
 
 vscode:
-  extensions: # based on nf-core.nf-core-extensionpack
+  extensions:
     - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                    # Nextflow syntax highlighting
+    - nextflow.nextflow # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
     - charliermarsh.ruff # Code linter Ruff

CHANGELOG.md

@@ -73,6 +73,7 @@
 - Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 ([#3122](https://github.com/nf-core/tools/pull/3122))
 - Update python:3.12-slim Docker digest to 59c7332 ([#3124](https://github.com/nf-core/tools/pull/3124))
+- Update gitpod setup ([#3136](https://github.com/nf-core/tools/pull/3136))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

nf_core/gitpod/gitpod.Dockerfile

@@ -1,6 +1,7 @@
 # Test build locally before making a PR
 #   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
 
+# See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
 FROM gitpod/workspace-base@sha256:f189a4195c3861365356f9c1b438ab26fd88e1ff46ce2843afc62861fc982e0c
 
 USER root
@@ -40,9 +41,8 @@ RUN chown -R gitpod:gitpod /opt/conda /usr/src/nf_core
 
 # Change user to gitpod
 USER gitpod
-# Install nextflow, nf-core, Mamba, and pytest-workflow
-RUN conda config --add channels defaults && \
-    conda config --add channels bioconda && \
+# Install nextflow, nf-core, nf-test, and other useful tools
+RUN conda config --add channels bioconda && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
     conda install --quiet --yes --name base \
@@ -63,3 +63,4 @@ RUN nextflow self-update && \
 # Setup pdiff for nf-test diffs
 ENV NFT_DIFF="pdiff"
 ENV NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
+ENV JAVA_TOOL_OPTIONS=

nf_core/pipeline-template/.gitpod.yml

@@ -4,9 +4,6 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-  - name: unset JAVA_TOOL_OPTIONS
-    command: |
-      unset JAVA_TOOL_OPTIONS
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
@@ -15,7 +12,7 @@ vscode:
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files{% endif %}
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                    # Nextflow syntax highlighting
+    - nextflow.nextflow # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
     - charliermarsh.ruff # Code linter Ruff