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Merge pull request #171 from nf-core/dev
release 2.1.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| name: nf-core CI external | ||
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
| on: | ||
| workflow_dispatch: | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
| CAPSULE_LOG: none | ||
|
|
||
| jobs: | ||
| netmhc: | ||
| name: Run NetMHC tool family tests | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| NXF_VER: ${{ matrix.nxf_ver }} | ||
| strategy: | ||
| matrix: | ||
| include: | ||
| # Test pipeline minimum Nextflow version | ||
| - NXF_VER: "21.10.3" | ||
| NXF_EDGE: "" | ||
| # Test latest edge release of Nextflow | ||
| - NXF_VER: "" | ||
| NXF_EDGE: "1" | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v2 | ||
|
|
||
| - name: Install non-free software | ||
| env: | ||
| DECRYPT_PASSPHRASE: ${{ secrets.TEST_NETMHC }} | ||
| run: | | ||
| mkdir -v non-free | ||
| curl -L https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/software/non-free-software.tar.gpg | ${GITHUB_WORKSPACE}/bin/decrypt | tar -C non-free -v -x | ||
| - name: Install Nextflow | ||
| env: | ||
| NXF_VER: ${{ matrix.NXF_VER }} | ||
| # Uncomment only if the edge release is more recent than the latest stable release | ||
| # See https://github.com/nextflow-io/nextflow/issues/2467 | ||
| # NXF_EDGE: ${{ matrix.NXF_EDGE }} | ||
| run: | | ||
| wget -qO- get.nextflow.io | bash | ||
| sudo mv nextflow /usr/local/bin/ | ||
| - name: Run pipeline with NetMHC | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test_netmhc,docker --outdir ./results | ||
| - name: Run pipeline with NetMHCpan | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test_netmhcpan,docker --outdir ./results |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| name: Fix linting from a comment | ||
| on: | ||
| issue_comment: | ||
| types: [created] | ||
|
|
||
| jobs: | ||
| deploy: | ||
| # Only run if comment is on a PR with the main repo, and if it contains the magic keywords | ||
| if: > | ||
| contains(github.event.comment.html_url, '/pull/') && | ||
| contains(github.event.comment.body, '@nf-core-bot fix linting') && | ||
| github.repository == 'nf-core/epitopeprediction' | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| # Use the @nf-core-bot token to check out so we can push later | ||
| - uses: actions/checkout@v3 | ||
| with: | ||
| token: ${{ secrets.nf_core_bot_auth_token }} | ||
|
|
||
| # Action runs on the issue comment, so we don't get the PR by default | ||
| # Use the gh cli to check out the PR | ||
| - name: Checkout Pull Request | ||
| run: gh pr checkout ${{ github.event.issue.number }} | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | ||
|
|
||
| - uses: actions/setup-node@v2 | ||
|
|
||
| - name: Install Prettier | ||
| run: npm install -g prettier @prettier/plugin-php | ||
|
|
||
| # Check that we actually need to fix something | ||
| - name: Run 'prettier --check' | ||
| id: prettier_status | ||
| run: | | ||
| if prettier --check ${GITHUB_WORKSPACE}; then | ||
| echo "::set-output name=result::pass" | ||
| else | ||
| echo "::set-output name=result::fail" | ||
| fi | ||
| - name: Run 'prettier --write' | ||
| if: steps.prettier_status.outputs.result == 'fail' | ||
| run: prettier --write ${GITHUB_WORKSPACE} | ||
|
|
||
| - name: Commit & push changes | ||
| if: steps.prettier_status.outputs.result == 'fail' | ||
| run: | | ||
| git config user.email "[email protected]" | ||
| git config user.name "nf-core-bot" | ||
| git config push.default upstream | ||
| git add . | ||
| git status | ||
| git commit -m "[automated] Fix linting with Prettier" | ||
| git push |
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