Ingest to phylogenetic #2

	name: Ingest to phylogenetic

	on:
	workflow_dispatch:

	jobs:
	ingest:
	permissions:
	id-token: write
	uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
	secrets: inherit
	with:
	# Starting with the default docker runtime
	# We can migrate to AWS Batch when/if we need to for more resources or if
	# the job runs longer than the GH Action limit of 6 hours.
	runtime: docker
	run: \|
	nextstrain build \
	--env AWS_ACCESS_KEY_ID \
	--env AWS_SECRET_ACCESS_KEY \
	ingest \
	--configfile build-configs/nextstrain-automation/config.yaml
	# Specifying artifact name to differentiate ingest build outputs from
	# the phylogenetic build outputs
	artifact-name: ingest-build-output
	artifact-paths: \|
	ingest/results/
	ingest/benchmarks/
	ingest/logs/
	ingest/.snakemake/log/

	# TKTK check for new data from ingest
	# This can potentially interface with GH and/or S3?
	# 1. Check last automated run's GH artifact output and diff with current S3 files
	# 2. Check S3's previous version of outputs and diff with current S3 files

	# TKTK phylo workflow
	# Just realized the phylo workflow does not have automated build uploads

	# phylogenetic:
	# needs: [ingest]
	# permissions:
	# id-token: write
	# uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
	# secrets: inherit
	# with:
	# runtime: docker
	# run: \|
	# nextstrain build \
	# --env AWS_ACCESS_KEY_ID \
	# --env AWS_SECRET_ACCESS_KEY \
	# phylogenetic \
	# --configfile build-configs/nextstrain-automation/config.yaml

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