Phylogenetic NCBI #3

	name: Phylogenetic NCBI

	defaults:
	run:
	# This is the same as GitHub Action's `bash` keyword as of 20 June 2023:
	# https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsshell
	#
	# Completely spelling it out here so that GitHub can't change it out from under us
	# and we don't have to refer to the docs to know the expected behavior.
	shell: bash --noprofile --norc -eo pipefail {0}

	on:
	workflow_dispatch:
	inputs:
	trial-name:
	description: \|
	Trial name for deploying builds.
	If not set, builds will overwrite existing builds at s3://nextstrain-data/avian-flu*
	If set, builds will be deployed to s3://nextstrain-staging/avian-flu_trials_<trial_name>_*
	required: false
	type: string

	jobs:
	phylogenetic:
	permissions:
	id-token: write
	uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
	secrets: inherit
	with:
	runtime: docker
	run: \|
	declare -a config;

	config+=(
	s3_src="s3://nextstrain-data/files/workflows/avian-flu/h5n1"
	);

	if [[ "$TRIAL_NAME" ]]; then
	config+=(
	deploy_url="s3://nextstrain-staging/avian-flu_trials_${TRIAL_NAME}_"
	)
	fi;

	nextstrain build \
	. \
	deploy_all \
	--snakefile Snakefile.genome \
	--config "${config[@]}"

	env: \|
	TRIAL_NAME: ${{ inputs.trial-name }}
	artifact-name: phylogenetic-full-genome-build-output

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