Mouse ONT R9 simulated uniform coverage polyA #151
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| name: Mouse ONT R9 simulated uniform coverage polyA | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '0 6 * * 5' | |
| env: | |
| RUN_NAME: Mouse.ONT_simulated.R9.uniform_cov.polyA | |
| LAUNCHER: ${{github.workspace}}/isoquant_tests/github/run_pipeline.py | |
| CFG_DIR: /abga/work/andreyp/ci_isoquant/data | |
| BIN_PATH: /abga/work/andreyp/ci_isoquant/bin/ | |
| OUTPUT_BASE: /abga/work/andreyp/ci_isoquant/output/${{github.ref_name}}/ | |
| concurrency: | |
| group: ${{github.workflow}} | |
| cancel-in-progress: false | |
| jobs: | |
| check-changes: | |
| runs-on: | |
| labels: [isoquant] | |
| name: 'Check for recent changes' | |
| outputs: | |
| has_changes: ${{steps.check.outputs.has_changes}} | |
| steps: | |
| - name: 'Checkout' | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: 'Check for commits in last 7 days' | |
| id: check | |
| run: | | |
| # Always run on manual trigger | |
| if [ "${{github.event_name}}" = "workflow_dispatch" ]; then | |
| echo "has_changes=true" >> $GITHUB_OUTPUT | |
| exit 0 | |
| fi | |
| # Check for commits in last 7 days | |
| COMMITS=$(git log --oneline --since="7 days ago" | wc -l) | |
| if [ "$COMMITS" -gt 0 ]; then | |
| echo "Found $COMMITS commits in last 7 days" | |
| echo "has_changes=true" >> $GITHUB_OUTPUT | |
| else | |
| echo "No commits in last 7 days, skipping" | |
| echo "has_changes=false" >> $GITHUB_OUTPUT | |
| fi | |
| launch-runner: | |
| needs: check-changes | |
| if: needs.check-changes.outputs.has_changes == 'true' | |
| runs-on: | |
| labels: [isoquant] | |
| name: 'Running IsoQuant and QC' | |
| steps: | |
| - name: 'Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: 'Checkout' | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - name: 'IsoQuant' | |
| if: always() | |
| shell: bash | |
| env: | |
| STEP_NAME: Mouse.ONT_simulated.R9.uniform_cov.polyA | |
| run: | | |
| export PATH=$PATH:${{env.BIN_PATH}} | |
| python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.yaml -o ${{env.OUTPUT_BASE}} | |