Phylogenetic #17
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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/zika* | |
If set, builds will be deployed to s3://nextstrain-staging/zika_trials_<trial_name>_* | |
required: false | |
type: string | |
sequences_url: | |
description: | | |
URL for a sequences.fasta.zst file. | |
If not provided, will use default sequences_url from phylogenetic/defaults/config_zika.yaml | |
required: false | |
type: string | |
metadata_url: | |
description: | | |
URL for a metadata.tsv.zst file. | |
If not provided, will use default metadata_url from phylogenetic/defaults/config_zika.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/zika_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/ |