Alignment with bowtie2 #26


	# Candace Savonen Jan 2024

	name: Render vignette with Docker image

	on:
	workflow_dispatch:
	pull_request:
	branches: [ main, staging ]
	push:
	branches: [ main, staging ]
	paths:
	- R/*
	- inst/extdata/*

	jobs:

	render-vignette:
	name: Render test
	runs-on: ubuntu-latest
	container:
	image: cansav09/gimap

	steps:
	- name: checkout
	uses: actions/checkout@v3
	with:
	fetch-depth: 0

	- name: Login as jhudsl-robot
	run: \|
	git config --global --add safe.directory $GITHUB_WORKSPACE
	git config --global user.email "itcrtrainingnetwork@gmail.com"
	git config --global user.name "jhudsl-robot"

	- name: Run vignette
	run: Rscript -e "rmarkdown::render('vignettes/getting-started.Rmd')"

	# Commit the rendered bookdown files
	- name: Commit rendered files
	env:
	GH_PAT: ${{ secrets.GH_PAT }}
	run: \|
	git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
	git fetch origin
	git add --force docs/*
	git commit -m 'Render vignette' \|\| echo "No changes to commit"
	git pull --allow-unrelated-histories --strategy-option=ours
	git push -u origin main \|\| echo "No changes to push"

Provide feedback