Update EBI index #13

	name: Update EBI index
	on:
	release:
	types: [published]
	workflow_dispatch:

	jobs:
	update_ebi_index:
	runs-on: ubuntu-latest
	permissions:
	contents: write
	pull-requests: write
	steps:
	- name: Store today date for further use
	id: today
	run: echo "date=$(date +%Y-%m-%d)" >> $GITHUB_OUTPUT
	- name: Check out the repo
	uses: actions/checkout@v3
	with:
	ref: develop
	- name: Run python script to get new dates
	id: index_updater
	run: echo "status=$(python EBI/update_index_json.py --release ${{ github.ref_name }} --release-date ${{ steps.today.outputs.date }})" >> $GITHUB_OUTPUT
	- name: Commit new change and push to develop branch
	if: ${{ steps.index_updater.outputs.status == 'updated' }}
	run: \|
	git config --local user.name ${{ github.actor }}
	git config --local user.email "${{ github.actor }}@users.noreply.github.com"
	git remote set-url origin https://${{ github.actor }}:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }}
	git add EBI/pathogens_portal_index.json
	git commit -m "EBI index updated"
	git push origin develop
	- name: Make pull request to main branch
	if: ${{ steps.index_updater.outputs.status == 'updated' }}
	env:
	GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	run: gh pr create --base main --head develop --title "Update EBI index - ${{ steps.today.outputs.date }}" --body "Version `${{ github.ref_name }}` is released, update index file accordingly."

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