Log and benchmark fixes #61
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| # This is a basic workflow adapted from the default Action worflow | |
| name: ARPEGGIO_run | |
| # Controls when the action will run. Triggers the workflow on push or pull request | |
| # events but only for the master branch. Added trigger to publishhed and created | |
| # releases as well | |
| on: | |
| push: | |
| pull_request: | |
| branches: [ master ] | |
| release: | |
| types: [ published, created ] | |
| # The workflow will have three jobs: running the main ARPEGGIO mode, linting and trying additional configs | |
| jobs: | |
| # Name of the job | |
| run-worfklow: | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-latest | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| - uses: actions/checkout@v3 | |
| # Run default snakemake | |
| - uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: '.' | |
| args: '--cores 1 --use-conda' | |
| run-linting: | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-latest | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| - uses: actions/checkout@v3 | |
| # Run default snakemake | |
| - uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: '.' | |
| args: '--lint' | |
| run-modes: | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-latest | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| - uses: actions/checkout@v3 | |
| # Run snakemake diploid only mode paired-end reads | |
| - name: run-ARPEGGIO-dp-PE | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: '.' | |
| args: '--configfile example/additional_config/config_dp_PE.yaml -n' | |
| # Run snakemake diploid only mode single-end reads | |
| - name: run-ARPEGGIO-dp-SE | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: '.' | |
| args: '--configfile example/additional_config/config_dp_SE.yaml -n' | |
| # Run snakemake polyploid only mode paired-end reads | |
| - name: run-ARPEGGIO-pp-PE | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: '.' | |
| args: '--configfile example/additional_config/config_pp_PE.yaml -n' | |
| # Run snakemake polyploid only mode single-end reads | |
| - name: run-ARPEGGIO-pp-SE | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: '.' | |
| args: '--configfile example/additional_config/config_pp_SE.yaml -n' |