Scheduled Run #1

	name: Map to GenBank Sequences
	run-name: ${{ github.event.inputs.reason \|\| 'Scheduled Run' }}
	on:
	schedule:
	- cron: '0 18 * * *'
	workflow_dispatch:
	inputs:
	reason:
	description: 'Reason for running the workflow'
	required: true
	default: 'Routine Processing'

	concurrency:
	group: ${{ github.repository }}

	jobs:
	map_to_genbank_seqs:
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash -el {0}
	steps:
	- name: Checkout code
	uses: actions/checkout@v4
	- name: Map to GenBank Sequences
	run: bash scripts/map_genbank.sh ${{ github.workspace }}/metadata/SraRunTable_automated.csv ${{ github.workspace }}/fasta/ > ${{ github.workspace }}/metadata/genbank_mapping.tsv
	- name: Push GenBank Mappings
	run: \|
	git config --global user.email "github-actions[bot]@users.noreply.github.com"
	git config --global user.name "github-actions[bot]"
	mv ${{ github.workspace }}/genbank_mapping.tsv ${{ github.workspace }}/metadata/genbank_mapping.tsv
	if [[ $(git status --porcelain ${{ github.workspace }}/metadata/genbank_mapping.tsv) ]]; then
	git add ${{ github.workspace }}/metadata/genbank_mapping.tsv
	git commit -m "Update GenBank mappings"
	git push
	fi

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