Ingest NCBI #26
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| name: Ingest NCBI | |
| 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: | |
| schedule: | |
| # Note times are in UTC, which is 1 or 2 hours behind CET depending on daylight savings. | |
| # | |
| # Note the actual runs might be late. | |
| # Numerous people were confused, about that, including me: | |
| # - https://github.community/t/scheduled-action-running-consistently-late/138025/11 | |
| # - https://github.com/github/docs/issues/3059 | |
| # | |
| # Note, '*' is a special character in YAML, so you have to quote this string. | |
| # | |
| # Docs: | |
| # - https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows#schedule | |
| # | |
| # Tool that deciphers this particular format of crontab string: | |
| # - https://crontab.guru/ | |
| # | |
| # Runs at 5pm UTC (1pm EDT/10am PDT) since curation by NCBI happens on the East Coast. | |
| # We were running into invalid zip archive errors at 9am PDT, so hoping an hour | |
| # delay will lower the error frequency | |
| - cron: '0 17 * * *' | |
| 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/trials/<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 [[ "$TRIAL_NAME" ]]; then | |
| # Create JSON string for the nested upload config | |
| S3_DST_BASE="s3://nextstrain-data/files/workflows/avian-flu/trial/$TRIAL_NAME" | |
| config+=( | |
| s3_dst=$( | |
| jq -cn --arg S3_DST_BASE "$S3_DST_BASE" '{ | |
| "joined-ncbi": "\($S3_DST_BASE)/h5n1", | |
| "ncbi": "\($S3_DST_BASE)/h5n1/ncbi", | |
| "andersen-lab": "\($S3_DST_BASE)/h5n1/andersen-lab" | |
| }' | |
| ) | |
| ) | |
| fi; | |
| nextstrain build \ | |
| ingest \ | |
| upload_all_ncbi \ | |
| --configfile build-configs/ncbi/defaults/config.yaml \ | |
| --config "${config[@]}" | |
| env: | | |
| NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }} | |
| TRIAL_NAME: ${{ inputs.trial-name }} | |
| # Specifying artifact name to differentiate ingest build outputs from | |
| # the phylogenetic build outputs | |
| artifact-name: ingest-ncbi-build-output | |
| artifact-paths: | | |
| ingest/.snakemake/log/ | |
| ingest/andersen-lab/results/ | |
| ingest/andersen-lab/benchmarks/ | |
| ingest/andersen-lab/logs/ | |
| ingest/joined-ncbi/results/ | |
| ingest/joined-ncbi/benchmarks/ | |
| ingest/joined-ncbi/logs/ | |
| ingest/ncbi/results/ | |
| ingest/ncbi/benchmarks/ | |
| ingest/ncbi/logs/ |