minimap2 preset for pacbio should be map-hifi (#441) #10

	name: build docs
	# https://github.com/nf-cmgg/structural/blob/master/.github/workflows/build-docs.yml
	on:
	push:
	branches:
	- master
	- main
	- dev
	permissions:
	contents: write
	jobs:
	deploy:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	with:
	fetch-depth: 0 # fetch all commits/branches
	- uses: actions/setup-python@v4
	with:
	python-version: 3.x
	- run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
	- name: Obtain version from nextflow config
	run: \|
	version=$(grep "version" nextflow.config \| tail -1 \| sed -e s'/[^=]*= //' \| cut -d "'" -f 2)
	[[ $version == "dev" ]] && pipeline_version="dev" \|\| pipeline_version=$version
	echo "pipeline_version=$pipeline_version" >> $GITHUB_ENV
	- name: Setup git user
	run: \|
	git config --global user.name "${{github.actor}}"
	git config --global user.email "${{github.actor}}@users.noreply.github.com"
	- uses: actions/cache@v3
	with:
	key: mkdocs-material-${{ env.cache_id }}
	path: .cache
	restore-keys: \|
	mkdocs-material-
	- name: Install dependencies
	run: pip install mkdocs-material pymdown-extensions pillow cairosvg mike
	- name: Build docs
	run: \|
	[[ ${{ env.pipeline_version }} == "dev" ]] && mike deploy --push ${{ env.pipeline_version }} \|\| mike deploy --push --update-aliases ${{ env.pipeline_version }} latest
	- name: Set default docs
	run: mike set-default --push latest

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