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ingest-to-phylo
Github workflow [#2]
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name: Ingest to phylogenetic | ||
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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} | ||
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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 * * *' | ||
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workflow_dispatch: | ||
inputs: | ||
ingest_image: | ||
description: 'Specific container image to use for ingest workflow (will override the default of "nextstrain build")' | ||
required: false | ||
phylogenetic_image: | ||
description: 'Specific container image to use for phylogenetic workflow (will override the default of "nextstrain build")' | ||
required: false | ||
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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 | ||
env: | | ||
NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.ingest_image }} | ||
run: | | ||
nextstrain build \ | ||
ingest \ | ||
upload_all \ | ||
--configfile build-configs/nextstrain-automation/config.yaml | ||
# Specifying artifact name to differentiate ingest build outputs from | ||
# the phylogenetic build outputs | ||
artifact-name: ingest-build-output | ||
artifact-paths: | | ||
ingest/results/ | ||
ingest/benchmarks/ | ||
ingest/logs/ | ||
ingest/.snakemake/log/ | ||
# Check if ingest results include new data by checking for the cache | ||
# of the file with the results' Metadata.sh256sum (which should have been added within upload-to-s3) | ||
# GitHub will remove any cache entries that have not been accessed in over 7 days, | ||
# so if the workflow has not been run over 7 days then it will trigger phylogenetic. | ||
check-new-data: | ||
needs: [ingest] | ||
runs-on: ubuntu-latest | ||
outputs: | ||
cache-hit: ${{ steps.check-cache.outputs.cache-hit }} | ||
steps: | ||
- name: Get sha256sum | ||
id: get-sha256sum | ||
env: | ||
AWS_DEFAULT_REGION: ${{ vars.AWS_DEFAULT_REGION }} | ||
run: | | ||
s3_urls=( | ||
"s3://nextstrain-data/files/workflows/yellow-fever/metadata.tsv.zst" | ||
"s3://nextstrain-data/files/workflows/yellow-fever/sequences.fasta.zst" | ||
) | ||
# Code below is modified from ingest/upload-to-s3 | ||
# https://github.com/nextstrain/ingest/blob/c0b4c6bb5e6ccbba86374d2c09b42077768aac23/upload-to-s3#L23-L29 | ||
no_hash=0000000000000000000000000000000000000000000000000000000000000000 | ||
for s3_url in "${s3_urls[@]}"; do | ||
s3path="${s3_url#s3://}" | ||
bucket="${s3path%%/*}" | ||
key="${s3path#*/}" | ||
s3_hash="$(aws s3api head-object --no-sign-request --bucket "$bucket" --key "$key" --query Metadata.sha256sum --output text 2>/dev/null || echo "$no_hash")" | ||
echo "${s3_hash}" | tee -a ingest-output-sha256sum | ||
done | ||
- name: Check cache | ||
id: check-cache | ||
uses: actions/cache@v4 | ||
with: | ||
path: ingest-output-sha256sum | ||
key: ingest-output-sha256sum-${{ hashFiles('ingest-output-sha256sum') }} | ||
lookup-only: true | ||
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phylogenetic: | ||
needs: [check-new-data] | ||
if: ${{ needs.check-new-data.outputs.cache-hit != 'true' }} | ||
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.phylogenetic_image }} | ||
run: | | ||
nextstrain build \ | ||
phylogenetic \ | ||
deploy_all \ | ||
--configfile build-configs/nextstrain-automation/config.yaml | ||
# 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/ |