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Phylogenetic

Phylogenetic #14

Workflow file for this run

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/