Skip to content

genbank/rebuild

genbank/rebuild #995

Workflow file for this run

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