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