Ingest #8
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name: Ingest | |
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 | |
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/dengue/ | |
If set, outputs will be uploaded to s3://nextstrain-data/files/workflows/dengue/trials/<trial_name>/ | |
required: false | |
type: string | |
jobs: | |
set_config_overrides: | |
runs-on: ubuntu-latest | |
steps: | |
- id: config | |
name: Set config overrides | |
env: | |
TRIAL_NAME: ${{ inputs.trial_name }} | |
run: | | |
config="" | |
if [[ "$TRIAL_NAME" ]]; then | |
config+="--config" | |
config+=" s3_dst='s3://nextstrain-data/files/workflows/dengue/trials/"$TRIAL_NAME"'" | |
fi | |
echo "config=$config" >> "$GITHUB_OUTPUT" | |
outputs: | |
config_overrides: ${{ steps.config.outputs.config }} | |
ingest: | |
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 \ | |
ingest \ | |
upload_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: ingest-build-output | |
artifact-paths: | | |
ingest/results/ | |
ingest/benchmarks/ | |
ingest/logs/ | |
ingest/.snakemake/log/ |