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Merge pull request #109 from sanger-tol/dev
1.3.0 Release
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| name: Test successful pipeline download with 'nf-core download' | ||
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| # Run the workflow when: | ||
| # - dispatched manually | ||
| # - when a PR is opened or reopened to master branch | ||
| # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. | ||
| on: | ||
| workflow_dispatch: | ||
| inputs: | ||
| testbranch: | ||
| description: "The specific branch you wish to utilize for the test execution of nf-core download." | ||
| required: true | ||
| default: "dev" | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| - edited | ||
| - synchronize | ||
| branches: | ||
| - main | ||
| - dev | ||
| pull_request_target: | ||
| branches: | ||
| - main | ||
| - dev | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
|
|
||
| jobs: | ||
| download: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v2 | ||
|
|
||
| - name: Disk space cleanup | ||
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | ||
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|
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| - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | ||
| with: | ||
| python-version: "3.12" | ||
| architecture: "x64" | ||
| - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 | ||
| with: | ||
| singularity-version: 3.8.3 | ||
|
|
||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install git+https://github.com/nf-core/tools.git@dev | ||
| - name: Get the repository name and current branch set as environment variable | ||
| run: | | ||
| echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} | ||
| echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} | ||
| echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} | ||
| - name: Download the pipeline | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| run: | | ||
| nf-core download ${{ env.REPO_LOWERCASE }} \ | ||
| --revision ${{ env.REPO_BRANCH }} \ | ||
| --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ | ||
| --compress "none" \ | ||
| --container-system 'singularity' \ | ||
| --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ | ||
| --container-cache-utilisation 'amend' \ | ||
| --download-configuration | ||
| - name: Inspect download | ||
| run: tree ./${{ env.REPOTITLE_LOWERCASE }} | ||
|
|
||
| - name: Run the downloaded pipeline (stub) | ||
| id: stub_run_pipeline | ||
| continue-on-error: true | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results | ||
| - name: Run the downloaded pipeline (stub run not supported) | ||
| id: run_pipeline | ||
| if: ${{ job.steps.stub_run_pipeline.status == failure() }} | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -2,6 +2,7 @@ | |
| work/ | ||
| data/ | ||
| results/ | ||
| null/ | ||
| .DS_Store | ||
| testing/ | ||
| testing* | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,14 +1,20 @@ | ||
| image: nfcore/gitpod:latest | ||
| tasks: | ||
| - name: Update Nextflow and setup pre-commit | ||
| 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 | ||
| # - cssho.vscode-svgviewer # SVG viewer | ||
| - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code | ||
| - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed | ||
| - 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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| repos: | ||
| - repo: https://github.com/pre-commit/mirrors-prettier | ||
| rev: "v3.1.0" | ||
| hooks: | ||
| - id: prettier | ||
| additional_dependencies: | ||
| - [email protected] | ||
|
|
||
| - repo: https://github.com/editorconfig-checker/editorconfig-checker.python | ||
| rev: "2.7.3" | ||
| hooks: | ||
| - id: editorconfig-checker | ||
| alias: ec |
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