feat(checkm2): upgrade checkm2 to version 2 #59

	# Forked from eKatchko/public-bioinformatics-databases

	name: Process changed files

	# Controls when the workflow will run
	on:
	pull_request:
	branches:
	- 'main'
	paths:
	- 'databases/**.json'
	workflow_dispatch:
	inputs:
	base:
	type: string
	required: true
	head:
	type: string
	required: true


	jobs:
	# This workflow contains a single job called "changed-files"
	changed-files:
	# The type of runner that the job will run on
	runs-on: [self-hosted, fts3-client-production ]
	environment: APPROVAL_REQUIRED

	# Steps represent a sequence of tasks that will be executed as part of the job
	steps:

	# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- name: Get changed files
	id: changed-files
	uses: tj-actions/changed-files@v41
	with:
	since_last_remote_commit: "true"
	files: \|
	databases/*.json

	- name: Get changed files with git diff and send to fts3-connector
	id: git-diff
	run: \|
	declare -a CHANGED=($(git diff --name-only -r origin/${{ github.base_ref \|\| github.event.inputs.base }} origin/${{ github.head_ref \|\| github.event.inputs.head }} \| grep databases/))
	for file in "${CHANGED[@]}"; do
	echo "Calling with $file"
	curl -H "X-AUTH-HEADER: ${{ secrets.FTS3_CLIENT_API_KEY }}" -H "Content-Type: application/json" -X POST -d @$file "${{ vars.FTS3_CLIENT_ENDPOINT }}/transfer/dry"
	done

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