actions just for ubuntu, medaka to env file #734

	name: piranha
	on: [push, pull_request]
	defaults:
	run:
	shell: bash -l {0}

	jobs:
	run_piranha_test:
	name: piranha test on ${{ matrix.os }}
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: ["ubuntu-latest"]
	steps:
	- uses: actions/checkout@v3
	- uses: conda-incubator/setup-miniconda@v3
	with:
	auto-update-conda: false
	environment-file: environment.yml
	activate-environment: piranha
	channels: conda-forge,bioconda,defaults
	miniforge-version: latest
	- name: Install piranha
	run: pip install -e .
	- name: Check piranha version
	run: piranha --version
	- name: Run piranha with test data
	run: piranha -i piranha/test/pak_run/demultiplexed --verbose -b piranha/test/pak_run/barcodes01.csv -t 2 2>&1 \| tee piranha.log
	- name: Run piranha with minimap2 option
	run: piranha -i piranha/test/pak_run/demultiplexed --verbose -b piranha/test/pak_run/barcodes01.csv -mo x=map-ont k=8 -t 2 2>&1 \| tee piranha.log
	- name: Run piranha in phylo mode
	run: piranha -i piranha/test/pak_run/demultiplexed --verbose -b piranha/test/pak_run/barcodes.csv -t 2 -rp -ud -sd piranha/test/supp_data 2>&1 \| tee piranha_phylo.log
	- name: Run piranha in haplo mode
	run: piranha -i piranha/test/pak_run/demultiplexed --verbose -b piranha/test/pak_run/barcodes01.csv -t 2 -rh 2>&1 \| tee piranha_haplo.log

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