Phylogenetic #39
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: Phylogenetic | |
| defaults: | |
| run: | |
| # This is the same as GitHub Action's `bash` keyword as of 20 June 2023: | |
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsshell | |
| # | |
| # Completely spelling it out here so that GitHub can't change it out from under us | |
| # and we don't have to refer to the docs to know the expected behavior. | |
| shell: bash --noprofile --norc -eo pipefail {0} | |
| on: | |
| workflow_call: | |
| inputs: | |
| image: | |
| description: 'Specific container image to use for phylogenetic workflow (will override the default of "nextstrain build")' | |
| required: false | |
| type: string | |
| workflow_dispatch: | |
| inputs: | |
| image: | |
| description: 'Specific container image to use for ingest workflow (will override the default of "nextstrain build")' | |
| required: false | |
| type: string | |
| trial_name: | |
| description: | | |
| Trial name for deploying builds. | |
| If not set, builds will overwrite existing builds at s3://nextstrain-data/dengue* | |
| If set, builds will be deployed to s3://nextstrain-staging/dengue_trials_<trial_name>_* | |
| required: false | |
| type: string | |
| sequences_url: | |
| description: | | |
| URL for sequences_{serotype}.fasta.zst files where {serotype} will be replaced by all, denv1 to denv4. | |
| If not provided, will use default sequences_url from phylogenetic/config/config_dengue.yaml | |
| required: false | |
| type: string | |
| metadata_url: | |
| description: | | |
| URL for metadata_{serotype}.tsv.zst files where {serotype} will be replaced by all, denv1 to denv4. | |
| If not provided, will use default metadata_url from phylogenetic/config/config_dengue.yaml | |
| required: false | |
| type: string | |
| jobs: | |
| set_config_overrides: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - id: config | |
| name: Set config overrides | |
| env: | |
| TRIAL_NAME: ${{ inputs.trial_name }} | |
| SEQUENCES_URL: ${{ inputs.sequences_url }} | |
| METADATA_URL: ${{ inputs.metadata_url }} | |
| run: | | |
| config="" | |
| if [[ "$TRIAL_NAME" ]]; then | |
| config+=" deploy_url='s3://nextstrain-staging/dengue_trials_"$TRIAL_NAME"_'" | |
| fi | |
| if [[ "$SEQUENCES_URL" ]]; then | |
| config+=" sequences_url='"$SEQUENCES_URL"'" | |
| fi | |
| if [[ "$METADATA_URL" ]]; then | |
| config+=" metadata_url='"$METADATA_URL"'" | |
| fi | |
| if [[ $config ]]; then | |
| config="--config $config" | |
| fi | |
| echo "config=$config" >> "$GITHUB_OUTPUT" | |
| outputs: | |
| config_overrides: ${{ steps.config.outputs.config }} | |
| phylogenetic: | |
| needs: [set_config_overrides] | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| # Starting with the default docker runtime | |
| # We can migrate to AWS Batch when/if we need to for more resources or if | |
| # the job runs longer than the GH Action limit of 6 hours. | |
| runtime: docker | |
| env: | | |
| NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }} | |
| CONFIG_OVERRIDES: ${{ needs.set_config_overrides.outputs.config_overrides }} | |
| run: | | |
| nextstrain build \ | |
| phylogenetic \ | |
| deploy_all \ | |
| --configfile build-configs/nextstrain-automation/config.yaml \ | |
| $CONFIG_OVERRIDES | |
| # Specifying artifact name to differentiate ingest build outputs from | |
| # the phylogenetic build outputs | |
| artifact-name: phylogenetic-build-output | |
| artifact-paths: | | |
| phylogenetic/auspice/ | |
| phylogenetic/results/ | |
| phylogenetic/benchmarks/ | |
| phylogenetic/logs/ | |
| phylogenetic/.snakemake/log/ |