Read grouping tests #108
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| name: Read grouping tests | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '0 2 * * 0,4' | |
| env: | |
| RUN_NAME: Resume_tests | |
| LAUNCHER: ${{github.workspace}}/tests/github/run_pipeline.py | |
| CFG_DIR: /abga/work/andreyp/ci_isoquant/data | |
| BIN_PATH: /abga/work/andreyp/ci_isoquant/bin/ | |
| OUTPUT_BASE: /abga/work/andreyp/ci_isoquant/output/${{github.ref_name}}/ | |
| concurrency: | |
| group: ${{github.workflow}} | |
| cancel-in-progress: false | |
| jobs: | |
| launch-runner: | |
| runs-on: | |
| labels: [isoquant] | |
| name: 'Running IsoQuant and QC' | |
| steps: | |
| - name: 'Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: 'Checkout' | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - name: 'Grouping by BAM tag' | |
| if: always() | |
| shell: bash | |
| env: | |
| STEP_NAME: GROUP1.TAG.SIRVs.R10 | |
| run: | | |
| export PATH=$PATH:${{env.BIN_PATH}} | |
| python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}} | |
| - name: 'Grouping by TSV file' | |
| if: always() | |
| shell: bash | |
| env: | |
| STEP_NAME: GROUP2.TSV.SIRVs.R10 | |
| run: | | |
| export PATH=$PATH:${{env.BIN_PATH}} | |
| python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}} | |
| - name: 'Grouping by read id' | |
| if: always() | |
| shell: bash | |
| env: | |
| STEP_NAME: GROUP3.READID.SIRVs.R10 | |
| run: | | |
| export PATH=$PATH:${{env.BIN_PATH}} | |
| python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}} | |
| - name: 'Grouping by file name' | |
| if: always() | |
| shell: bash | |
| env: | |
| STEP_NAME: GROUP4.FILES.SIRVs.R10 | |
| run: | | |
| export PATH=$PATH:${{env.BIN_PATH}} | |
| python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}} | |
| - name: 'Grouping by CSV file' | |
| if: always() | |
| shell: bash | |
| env: | |
| STEP_NAME: GROUP5.CSV.SIRVs.R10 | |
| run: | | |
| export PATH=$PATH:${{env.BIN_PATH}} | |
| python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}} | |