Replace custom containers with seqera containers incl version upgrades #72

	name: pca_roh

	on:
	push:
	paths-ignore:
	- 'README.md'
	- 'LICENSE.md'
	- 'workflow/rules/1.2_map_to_mitogenomes.smk'
	- 'workflow/rules/7_mlRho.smk'
	- 'workflow/rules/12_snpEff.smk'
	- 'workflow/rules/13_GERP.smk'
	branches:
	- main
	pull_request:
	paths-ignore:
	- 'README.md'
	- 'LICENSE.md'
	- 'workflow/docker'
	- 'workflow/rules/1.2_map_to_mitogenomes.smk'
	- 'workflow/rules/7_mlRho.smk'
	- 'workflow/rules/12_snpEff.smk'
	- 'workflow/rules/13_GERP.smk'
	branches:
	- main
	- dev

	jobs:
	test:
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v3

	- uses: eWaterCycle/setup-apptainer@v2
	with:
	apptainer-version: 1.1.4

	- uses: conda-incubator/setup-miniconda@v2
	with:
	miniforge-variant: Mambaforge
	channels: conda-forge,bioconda
	activate-environment: generode
	environment-file: environment.yml
	auto-activate-base: false

	- name: conda_environment
	shell: bash -l {0}
	run: \|
	conda info
	conda list

	- name: Free Up GitHub Actions Ubuntu Runner Disk Space 🔧
	uses: jlumbroso/free-disk-space@main
	with:
	# This might remove tools that are actually needed, if set to "true" but frees about 6 GB
	tool-cache: false

	# All of these default to true, but feel free to set to "false" if necessary for your workflow
	android: true
	dotnet: true
	haskell: true
	large-packages: true
	swap-storage: true

	- name: pca_roh_dry
	shell: bash -l {0}
	run: \|
	snakemake -np -k --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity

	- name: pca_roh
	shell: bash -l {0}
	run: \|
	snakemake -k --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity

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