Merge pull request #2569 from mirpedrol/gitpod

Unset env variable JAVA_TOOL_OPTIONS in gitpod

.github/workflows/pytest.yml

@@ -39,16 +39,6 @@ jobs:
         id: conditions
         run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> $GITHUB_ENV
 
-      - name: Check out source-code repository
-        uses: actions/checkout@v4
-        if: ${{ env.run-tests == 'true' }}
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
-        if: ${{ env.run-tests == 'true' }}
     outputs:
       python-version: ${{ matrix.python-version }}
       runner: ${{ matrix.runner }}
@@ -97,7 +87,7 @@ jobs:
           path: |
             /usr/local/bin/nf-test
             /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+          key: ${{ runner.os }}-nftest-${{ env.date }}
 
       - name: Install nf-test
         if: steps.cache-software.outputs.cache-hit != 'true'

.gitpod.yml

@@ -6,6 +6,9 @@ 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
     - codezombiech.gitignore # Language support for .gitignore files

CHANGELOG.md

@@ -8,6 +8,7 @@
 - Fancier syntax highlighting for example samplesheets in the usage.md template ([#2503](https://github.com/nf-core/tools/pull/2503))
 - Use closure for multiqc ext.args ([#2509](https://github.com/nf-core/tools/pull/2509))
 - Fix how the modules template references the conda environment file ([#2540](https://github.com/nf-core/tools/pull/2540))
+- Unset env variable JAVA_TOOL_OPTIONS in gitpod ([#2569](https://github.com/nf-core/tools/pull/2569))
 
 ### Download
 
@@ -41,6 +42,7 @@
 - Add mypy to pre-commit config for the tools repo ([#2545](https://github.com/nf-core/tools/pull/2545))
 - Use Path objects for ComponentCreate and update the structure of components templates ([#2551](https://github.com/nf-core/tools/pull/2551)).
 - GitPod base image: swap tool installation back to `conda` from `mamba` ([#2566](https://github.com/nf-core/tools/pull/2566)).
+- Unset env variable JAVA_TOOL_OPTIONS in gitpod ([#2569](https://github.com/nf-core/tools/pull/2569))
 
 # [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25]
 

nf_core/pipeline-template/.gitpod.yml

@@ -4,7 +4,9 @@ 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
     - codezombiech.gitignore # Language support for .gitignore files