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Add Clade-I GitHub action
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Following the hmpxv1 action, but using the docker runtime as the size of
the dataset allows us to rerun it on the action runner directly.
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jameshadfield committed Jun 18, 2024
1 parent 1140955 commit ec5aa8b
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59 changes: 59 additions & 0 deletions .github/workflows/rebuild-clade-i.yaml
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name: Rebuild clade-I

on:
repository_dispatch:
types:
- rebuild
- rebuild_clade-i

workflow_dispatch:
inputs:
trial_name:
description: "If set, result will be at nextstrain.org/staging/trial/${trial_name}/${auspice_name}"
required: false

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+=" deploy_url='s3://nextstrain-staging/'"
config+=" auspice_prefix='"$TRIAL_NAME"'"
fi
echo "config=$config" >> "$GITHUB_OUTPUT"
outputs:
config_overrides: ${{ steps.config.outputs.config }}

rebuild_clade_i:
needs: [set_config_overrides]
permissions:
id-token: write
uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
secrets: inherit
with:
# We can migrate to AWS Batch when/if we need to for more resources,
# but at the time of writing the clade-I build is small & quick
runtime: docker
env: |
CONFIG_OVERRIDES: ${{ needs.set_config_overrides.outputs.config_overrides }}
GITHUB_RUN_ID: ${{ github.run_id }}
SLACK_CHANNELS: ${{ inputs.trial_name && vars.TEST_SLACK_CHANNEL || vars.SLACK_CHANNELS }}
BUILD_DIR: phylogenetic
BUILD_NAME: clade-i
run: |
nextstrain build \
--env GITHUB_RUN_ID \
--env SLACK_TOKEN \
--env SLACK_CHANNELS \
. \
notify_on_deploy \
--configfiles $BUILD_DIR/defaults/$BUILD_NAME/config.yaml $BUILD_DIR/build-configs/nextstrain-automation/config.yaml \
$CONFIG_OVERRIDES --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile

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