planemo still requires samtools #178

	name: Planemo
	on: [push, pull_request]

	env:
	GALAXY_BRANCH: release_24.1

	defaults:
	run:
	shell: bash -l {0}

	jobs:
	planemo_test:
	name: Planemo test
	runs-on: ubuntu-latest
	strategy:
	matrix:
	chunk: [1, 2, 3]
	steps:
	- uses: actions/checkout@v4
	- uses: conda-incubator/setup-miniconda@v3
	with:
	miniconda-version: "latest"
	auto-activate-base: true
	python-version: "3.12"
	- name: get samtools
	run: \|
	conda install -c bioconda samtools
	- name: pip install
	run: \|
	pip install .[actions]
	- name: planemo
	run: \|
	./.planemo.sh ${{ matrix.chunk }} ${{ env.GALAXY_BRANCH }}
	- uses: actions/upload-artifact@v4
	with:
	name: 'Tool test output ${{ matrix.chunk }}'
	path: upload
	planemo_combine_outputs:
	name: Combine chunked test results
	needs: planemo_test
	runs-on: ubuntu-latest
	# strategy:
	# matrix:
	# python-version: ['3.8', '3.11']
	steps:
	- uses: actions/download-artifact@v4
	with:
	path: artifacts
	# - uses: actions/setup-python@v5
	# with:
	# python-version: ${{ matrix.python-version }}
	# - name: Cache .cache/pip
	# uses: actions/cache@v3
	# id: cache-pip
	# with:
	# path: ~/.cache/pip
	# key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ env.GALAXY_BRANCH }}
	- name: Combine outputs
	uses: galaxyproject/planemo-ci-action@v1
	id: combine
	with:
	mode: combine
	html-report: true
	- uses: actions/upload-artifact@v4
	with:
	name: 'All tool test results'
	path: upload
	- name: Check outputs
	uses: galaxyproject/planemo-ci-action@v1
	id: check
	with:
	mode: check

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