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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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name: Rebuild clade-I | ||
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on: | ||
repository_dispatch: | ||
types: | ||
- rebuild | ||
- rebuild_clade-i | ||
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workflow_dispatch: | ||
inputs: | ||
trial_name: | ||
description: "If set, result will be at nextstrain.org/staging/trial/${trial_name}/${auspice_name}" | ||
required: false | ||
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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 }} | ||
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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 |