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rebuild

rebuild #345

name: Rebuild hmpxv1
on:
repository_dispatch:
types:
- rebuild
- rebuild_hmpxv1
workflow_dispatch:
inputs:
trial_name:
description: "If set, result will be at nextstrain.org/staging/trial/${trial_name}/${auspice_name}"
required: false
image:
description: 'Specific container image to use for build (will override the default of "nextstrain build")'
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_hmpxv1:
needs: [set_config_overrides]
permissions:
id-token: write
uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
secrets: inherit
with:
runtime: aws-batch
env: |
NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }}
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: hmpxv1
run: |
nextstrain build \
--detach \
--no-download \
--cpus 8 \
--memory 32gib \
--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