Move fetch_sequences.smk to fetch_from_ncbi.smk #228
Workflow file for this run
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| name: CI | |
| on: | |
| - push | |
| - pull_request | |
| jobs: | |
| pathogen-ci: | |
| strategy: | |
| matrix: | |
| runtime: [docker, conda] | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| runtime: ${{ matrix.runtime }} | |
| run: | | |
| nextstrain build \ | |
| phylogenetic \ | |
| --configfile profiles/ci/profiles_config.yaml | |
| artifact-name: output-${{ matrix.runtime }} | |
| artifact-paths: | | |
| phylogenetic/auspice/ | |
| phylogenetic/results/ | |
| phylogenetic/benchmarks/ | |
| phylogenetic/logs/ | |
| phylogenetic/.snakemake/log/ |