genbank/rebuild #1021
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name: Rebuild open (GenBank) phylogenetic datasets | |
on: | |
# This workflow can be triggered from repository_dispatch events, | |
# for instance, after the appropriate preprocessing actions have completed | |
repository_dispatch: | |
types: | |
- rebuild | |
- open/rebuild | |
- genbank/rebuild | |
# Manually triggered using GitHub's UI | |
workflow_dispatch: | |
inputs: | |
trial_name: | |
description: "Short name for this trial build, for prefixing the uploaded data and results files. WARNING: without this we will overwrite files in s3://nextstrain-data/files/ncov/open/ and the trees on nextstrain.org/ncov/open/..." | |
required: false | |
image: | |
description: 'Specific container image to use for build (will override the default of "nextstrain build")' | |
required: false | |
jobs: | |
open: | |
permissions: | |
id-token: write | |
uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
secrets: inherit | |
with: | |
runtime: aws-batch | |
env: | | |
TRIAL_NAME: ${{ github.event.inputs.trial_name }} | |
NEXTSTRAIN_DOCKER_IMAGE: ${{ github.event.inputs.image }} | |
run: | | |
set -x | |
declare -a config | |
config+=(build_date=\'$(date +'%Y-%m-%d')\') | |
if [[ "$TRIAL_NAME" ]]; then | |
config+=( | |
S3_DST_BUCKET=nextstrain-staging/files/ncov/open/trial/"$TRIAL_NAME" | |
deploy_url=s3://nextstrain-staging/ | |
auspice_json_prefix=ncov_open_trial_"$TRIAL_NAME" | |
) | |
else | |
config+=(slack_token=$SLACK_TOKEN) | |
fi | |
nextstrain build \ | |
--detach \ | |
--cpus 72 \ | |
--memory 140GiB \ | |
. \ | |
deploy \ | |
upload \ | |
--config "${config[@]}" \ | |
--profile nextstrain_profiles/nextstrain-open \ | |
--set-threads tree=8 |