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Merge pull request #11 from sanger-tol/dev
Release 2.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| { | ||
| "name": "nfcore", | ||
| "image": "nfcore/gitpod:latest", | ||
| "remoteUser": "gitpod", | ||
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| // Configure tool-specific properties. | ||
| "customizations": { | ||
| // Configure properties specific to VS Code. | ||
| "vscode": { | ||
| // Set *default* container specific settings.json values on container create. | ||
| "settings": { | ||
| "python.defaultInterpreterPath": "/opt/conda/bin/python", | ||
| "python.linting.enabled": true, | ||
| "python.linting.pylintEnabled": true, | ||
| "python.formatting.autopep8Path": "/opt/conda/bin/autopep8", | ||
| "python.formatting.yapfPath": "/opt/conda/bin/yapf", | ||
| "python.linting.flake8Path": "/opt/conda/bin/flake8", | ||
| "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", | ||
| "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", | ||
| "python.linting.pylintPath": "/opt/conda/bin/pylint" | ||
| }, | ||
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| // Add the IDs of extensions you want installed when the container is created. | ||
| "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,4 @@ | ||
| *.config linguist-language=nextflow | ||
| *.nf.test linguist-language=nextflow | ||
| modules/nf-core/** linguist-generated | ||
| modules/sanger-tol/** linguist-generated | ||
| subworkflows/nf-core/** linguist-generated | ||
| subworkflows/sanger-tol/** linguist-generated |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| name: "Close user-tagged issues and PRs" | ||
| on: | ||
| schedule: | ||
| - cron: "0 0 * * 0" # Once a week | ||
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| jobs: | ||
| clean-up: | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| issues: write | ||
| pull-requests: write | ||
| steps: | ||
| - uses: actions/stale@v7 | ||
| with: | ||
| stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." | ||
| stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." | ||
| close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." | ||
| days-before-stale: 30 | ||
| days-before-close: 20 | ||
| days-before-pr-close: -1 | ||
| any-of-labels: "awaiting-changes,awaiting-feedback" | ||
| exempt-issue-labels: "WIP" | ||
| exempt-pr-labels: "WIP" | ||
| repo-token: "${{ secrets.GITHUB_TOKEN }}" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -8,23 +8,23 @@ jobs: | |
| # 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') && | ||
| contains(github.event.comment.body, '@sanger-tolsoft fix linting') && | ||
| github.repository == 'sanger-tol/ensemblrepeatdownload' | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| # Use the @nf-core-bot token to check out so we can push later | ||
| # Use the @sanger-tolsoft token to check out so we can push later | ||
| - uses: actions/checkout@v3 | ||
| with: | ||
| token: ${{ secrets.nf_core_bot_auth_token }} | ||
| token: ${{ secrets.sangertolsoft_access_token }} | ||
|
|
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| # 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 }} | ||
| GITHUB_TOKEN: ${{ secrets.sangertolsoft_access_token }} | ||
|
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| - uses: actions/setup-node@v2 | ||
| - uses: actions/setup-node@v3 | ||
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| - name: Install Prettier | ||
| run: npm install -g prettier @prettier/plugin-php | ||
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@@ -34,9 +34,9 @@ jobs: | |
| id: prettier_status | ||
| run: | | ||
| if prettier --check ${GITHUB_WORKSPACE}; then | ||
| echo "::set-output name=result::pass" | ||
| echo "result=pass" >> $GITHUB_OUTPUT | ||
| else | ||
| echo "::set-output name=result::fail" | ||
| echo "result=fail" >> $GITHUB_OUTPUT | ||
| fi | ||
| - name: Run 'prettier --write' | ||
|
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@@ -46,8 +46,8 @@ jobs: | |
| - 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 user.email "[email protected]" | ||
| git config user.name "sanger-tolsoft" | ||
| git config push.default upstream | ||
| git add . | ||
| git status | ||
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| name: sanger-tol LSF tests | ||
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| on: | ||
| workflow_dispatch: | ||
| jobs: | ||
| run-tower: | ||
| name: Run LSF tests | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Launch workflow via tower | ||
| uses: seqeralabs/action-tower-launch@v2 | ||
| with: | ||
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | ||
| access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} | ||
| compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} | ||
| revision: ${{ github.sha }} | ||
| workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ github.sha }} | ||
| parameters: | | ||
| { | ||
| "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ github.sha }}", | ||
| } | ||
| profiles: test,sanger,singularity,cleanup | ||
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| - uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: Tower debug log file | ||
| path: | | ||
| tower_action_*.log | ||
| tower_action_*.json |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| name: sanger-tol LSF full size tests | ||
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| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| - dev | ||
| workflow_dispatch: | ||
| jobs: | ||
| run-tower: | ||
| name: Run LSF full size tests | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Sets env vars for push | ||
| run: | | ||
| echo "REVISION=${{ github.sha }}" >> $GITHUB_ENV | ||
| if: github.event_name == 'push' | ||
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| - name: Sets env vars for workflow_dispatch | ||
| run: | | ||
| echo "REVISION=${{ github.sha }}" >> $GITHUB_ENV | ||
| if: github.event_name == 'workflow_dispatch' | ||
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| - name: Launch workflow via tower | ||
| uses: seqeralabs/action-tower-launch@v2 | ||
| with: | ||
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | ||
| access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} | ||
| compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} | ||
| revision: ${{ env.REVISION }} | ||
| workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ env.REVISION }} | ||
| parameters: | | ||
| { | ||
| "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}", | ||
| } | ||
| profiles: test_full,sanger,singularity,cleanup | ||
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| - uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: Tower debug log file | ||
| path: | | ||
| tower_action_*.log | ||
| tower_action_*.json |
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