fixed indices #36

	name: build-github-pages
	env:
	GITHUB_ACTOR: BackofenLab
	GITHUB_REPOSITORY: BackofenLab/V_RNA-pages
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

	on:
	push:
	branches:
	- main

	# Allows you to run this workflow manually from the Actions tab
	workflow_dispatch:

	# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
	permissions:
	contents: write
	pages: write
	id-token: write

	jobs:
	build_rmarkdown_job:
	runs-on: ubuntu-latest
	steps:
	- name: Get prerequisites and clone repository
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	run: \|
	set -x
	sudo apt-get update
	sudo apt-get install -y git
	git clone "https://token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" .
	shell: bash

	- name: create environment with mamba
	uses: conda-incubator/setup-miniconda@v2
	with:
	channels: conda-forge,defaults
	auto-activate-base: false
	activate-environment: rmarkdown-env
	environment-file: .github/envs/environment.yml

	- name: Render Rmd files
	run: \|
	eval "$(conda shell.bash hook)"
	conda activate rmarkdown-env
	Rscript -e "rmarkdown::render_site()"

	- name: Upload artifact
	uses: actions/upload-pages-artifact@v2
	with:
	# Upload entire repository
	path: 'docs/'

	- name: Deploy to GitHub Pages
	id: deployment
	uses: actions/deploy-pages@v2

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