Read grouping tests #121
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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}} | |