Merge pull request #110 from CCBR/dev #47
Workflow file for this run
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| name: test | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| pull_request: | |
| branches: | |
| - master | |
| - dev | |
| jobs: | |
| deploy: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/[email protected] | |
| - uses: docker://snakemake/snakemake:v7.19.1 | |
| with: | |
| directory: '.test' | |
| - name: dryrun | |
| shell: bash {0} | |
| run: | | |
| bash ./install.sh ./test-workdir/carlisle-v9999.9999.9999-dev | |
| ./test-workdir/carlisle-v9999.9999.9999-dev/bin/carlisle --runmode=init --workdir=./test-workdir/output_carlisle | |
| cp ./test-workdir/carlisle-v9999.9999.9999-dev/bin/.test/config_lint.yaml ./test-workdir/output_carlisle/config/config.yaml | |
| # TODO: use `carlisle run --mode dryrun` | |
| docker run -v ./test-workdir/:/opt2 snakemake/snakemake:v7.19.1 /bin/bash -c \ | |
| "cd /opt2 && snakemake \ | |
| -s ./carlisle-v9999.9999.9999-dev/bin/workflow/Snakefile \ | |
| --dryrun \ | |
| --configfile carlisle-v9999.9999.9999-dev/bin/.test/config_lint.yaml \ | |
| --directory output_carlisle" |