Rebuild GISAID phylogenetic datasets #785

	name: Rebuild GISAID 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
	- gisaid/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-ncov-private and the trees on nextstrain.org/ncov/gisaid..."
	required: false
	image:
	description: 'Specific container image to use for build (will override the default of "nextstrain build")'
	required: false

	jobs:
	gisaid:
	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-ncov-private/trial/"$TRIAL_NAME"
	deploy_url=s3://nextstrain-staging/
	auspice_json_prefix=ncov_gisaid_trial_"$TRIAL_NAME"
	)
	else
	config+=(slack_token=$SLACK_TOKEN)
	fi

	nextstrain build \
	--detach \
	--cpus 72 \
	--memory 140GiB \
	. \
	deploy \
	upload \
	--config "${config[@]}" \
	--profile nextstrain_profiles/nextstrain-gisaid \
	--set-threads tree=8

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