Run GenoFLU on curated GISAID data #43
This file contains hidden or 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: Run GenoFLU on curated GISAID data | |
| 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 ingest workflow (will override the default of "nextstrain build")' | |
| required: false | |
| type: string | |
| # The workflow_dispatch will be triggered by seasonal-flu when a new curated dataset is available | |
| # <https://github.com/nextstrain/seasonal-flu/blob/master/.github/workflows/upload.yaml> | |
| 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 outputs. | |
| If not set, outputs will overwrite files at s3://nextstrain-data/files/workflows/avian-flu/ | |
| If set, outputs will be uploaded to s3://nextstrain-data/files/workflows/avian-flu/trial/<trial_name>/ | |
| required: false | |
| type: string | |
| jobs: | |
| ingest: | |
| 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 | |
| run: | | |
| declare -a config; | |
| if [[ "$TRIAL_NAME" ]]; then | |
| # Create JSON string for the nested upload config | |
| S3_DST="s3://nextstrain-data-private/files/workflows/avian-flu/trial/$TRIAL_NAME" | |
| config+=( | |
| s3_dst=$(jq -cn --arg S3_DST "$S3_DST" '{"gisaid": $S3_DST}') | |
| ) | |
| fi; | |
| nextstrain build \ | |
| ingest \ | |
| --snakefile gisaid/Snakefile \ | |
| upload_all \ | |
| --config "${config[@]}" | |
| env: | | |
| NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }} | |
| TRIAL_NAME: ${{ inputs.trial_namee }} | |
| # Explicitly excluding `ingest/gisaid/results` and `ingest/gisaid/data` | |
| # since this is private data and should not available through the public artifacts | |
| artifact-name: genoflu-gisaid | |
| artifact-paths: | | |
| ingest/.snakemake/log/ | |
| ingest/gisaid/logs/ | |
| ingest/gisaid/benchmarks/ | |
| !ingest/gisaid/results | |
| !ingest/gisaid/data |