Updating the different GH actions #53

Workflow file for this run

.github/workflows/main_test.yaml at 48fcac9

	name: ashleys-qc-pipeline workflow checks

	on:
	push:
	branches:
	- "**"

	jobs:

	Formatting:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Formatting using Super-Linter
	uses: github/super-linter@v4
	env:
	VALIDATE_ALL_CODEBASE: false
	DEFAULT_BRANCH: master
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	VALIDATE_SNAKEMAKE_SNAKEFMT: true


	Linting:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository with submodules
	uses: actions/checkout@v4
	with:
	submodules: 'recursive' # Ensures all submodules are checked out
	lfs: true # Ensures LFS objects for the main repo are pulled

	- name: Pull LFS objects in submodules
	run: \|
	git submodule foreach --recursive 'git lfs pull'

	- name: List contents of .tests
	run: \|
	tree -h .tests

	- name: List contents of workflow/data
	run: \|
	tree -h workflow/data

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.12'

	- name: Add Conda to system path
	run: \|
	echo $CONDA/bin >> $GITHUB_PATH

	- name: Install dependencies
	run: \|
	conda install -c conda-forge mamba

	- name: Setup snakemake
	run: \|
	mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http

	- name: Run Snakemake Lint
	run: \|
	snakemake --lint

	Testing-basic:
	runs-on: ubuntu-latest
	needs:
	- Formatting
	- Linting
	steps:
	- name: Checkout repository with submodules and LFS
	uses: actions/checkout@v4
	with:
	submodules: recursive
	lfs: true

	- name: Pull LFS objects in submodules
	run: git submodule foreach --recursive 'git lfs pull'

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.12'

	- name: List contents of .tests
	run: \|
	tree -h .tests

	- name: List contents of workflow/data
	run: \|
	tree -h workflow/data

	- name: Add Conda to system path
	run: echo "$CONDA/bin" >> $GITHUB_PATH

	- name: Install dependencies
	run: conda install -c conda-forge mamba

	- name: Setup Snakemake
	run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http

	- name: List options of workflow
	run: \|
	snakemake --cores 1 --config list_commands=True --verbose --debug

	- name: Run workflow
	run: \|
	snakemake --cores 1 --software-deployment-method conda --configfile .tests/config/simple_config_ashleys.yaml \
	--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

	Testing-basic-with-slurm:
	runs-on: ubuntu-latest
	needs:
	- Formatting
	- Linting
	- Testing-basic
	services:
	mysql:
	image: mysql:8.0
	env:
	MYSQL_ROOT_PASSWORD: root
	ports:
	- "8888:3306"
	options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3

	steps:
	- uses: actions/checkout@v3

	- uses: koesterlab/setup-slurm-action@v1

	- name: Checkout repository with submodules and LFS
	uses: actions/checkout@v4
	with:
	submodules: recursive
	lfs: true

	- name: Pull LFS objects in submodules
	run: git submodule foreach --recursive 'git lfs pull'

	- name: List contents of .tests
	run: \|
	tree -h .tests

	- name: List contents of workflow/data
	run: \|
	tree -h workflow/data

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.12'

	- name: Add Conda to system path
	run: echo "$CONDA/bin" >> $GITHUB_PATH

	- name: Install dependencies
	run: conda install -c conda-forge mamba

	- name: Setup Snakemake with SLURM support
	run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http snakemake-executor-plugin-slurm

	- name: Run workflow on SLURM
	run: \|
	snakemake -j 1 -c 1 --executor slurm --workflow-profile .tests/config/slurm_config/ --verbose --debug \
	--software-deployment-method conda --conda-frontend mamba --configfile .tests/config/simple_config_ashleys.yaml -p --snakefile workflow/Snakefile

	Testing-with-MultiQC:
	runs-on: ubuntu-latest
	needs:
	- Formatting
	- Linting
	- Testing-basic
	steps:
	- name: Checkout repository with submodules and LFS
	uses: actions/checkout@v4
	with:
	submodules: recursive
	lfs: true

	- name: Pull LFS objects in submodules
	run: git submodule foreach --recursive 'git lfs pull'

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.12'

	- name: Add Conda to system path
	run: echo "$CONDA/bin" >> $GITHUB_PATH

	- name: Install dependencies
	run: conda install -c conda-forge mamba

	- name: Setup Snakemake
	run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http

	- name: List options of workflow
	run: \|
	snakemake --cores 1 --config list_commands=True --verbose --debug

	- name: Run workflow
	run: \|
	snakemake --cores 1 --software-deployment-method conda --configfile .tests/config/simple_config_ashleys.yaml --config MultiQC=True \
	--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

	Testing-with-ms-norm:
	runs-on: ubuntu-latest
	needs:
	- Formatting
	- Linting
	- Testing-basic
	steps:
	- name: Checkout repository with submodules and LFS
	uses: actions/checkout@v4
	with:
	submodules: recursive
	lfs: true

	- name: Pull LFS objects in submodules
	run: git submodule foreach --recursive 'git lfs pull'

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.12'

	- name: Add Conda to system path
	run: echo "$CONDA/bin" >> $GITHUB_PATH

	- name: Install dependencies
	run: conda install -c conda-forge mamba

	- name: Setup Snakemake
	run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http

	- name: List options of workflow
	run: \|
	snakemake --cores 1 --config list_commands=True --verbose --debug

	- name: Run workflow
	run: \|
	snakemake --cores 1 --software-deployment-method conda --configfile .tests/config/simple_config_ashleys.yaml --config multistep_normalisation=True \
	--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

	Testing-with-hg38:
	runs-on: ubuntu-latest
	needs:
	- Formatting
	- Linting
	- Testing-basic
	steps:
	- name: Checkout repository with submodules and LFS
	uses: actions/checkout@v4
	with:
	submodules: recursive
	lfs: true

	- name: Pull LFS objects in submodules
	run: git submodule foreach --recursive 'git lfs pull'

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.12'

	- name: Add Conda to system path
	run: echo "$CONDA/bin" >> $GITHUB_PATH

	- name: Install dependencies
	run: conda install -c conda-forge mamba

	- name: Setup Snakemake
	run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http

	- name: List options of workflow
	run: \|
	snakemake --cores 1 --config list_commands=True --verbose --debug

	- name: Run workflow
	run: \|
	snakemake --cores 1 --software-deployment-method conda --config reference=hg38 use_light_data=True chromosomes=[chr17] \
	--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

	Testing-with-hg19:
	runs-on: ubuntu-latest
	needs:
	- Formatting
	- Linting
	- Testing-basic
	- Testing-basic-with-slurm
	steps:
	- name: Checkout repository with submodules and LFS
	uses: actions/checkout@v4
	with:
	submodules: recursive
	lfs: true

	- name: Pull LFS objects in submodules
	run: git submodule foreach --recursive 'git lfs pull'

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.12'

	- name: Add Conda to system path
	run: echo "$CONDA/bin" >> $GITHUB_PATH

	- name: Install dependencies
	run: conda install -c conda-forge mamba

	- name: Setup Snakemake
	run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http

	- name: List options of workflow
	run: \|
	snakemake --cores 1 --config list_commands=True --verbose --debug

	- name: Run workflow
	run: \|
	snakemake --cores 1 --software-deployment-method conda --config reference=hg19 use_light_data=True chromosomes=[chr17] \
	--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

	Testing-with-T2T:
	runs-on: ubuntu-latest
	needs:
	- Formatting
	- Linting
	- Testing-basic
	- Testing-basic-with-slurm
	steps:
	- name: Checkout repository with submodules and LFS
	uses: actions/checkout@v4
	with:
	submodules: recursive
	lfs: true

	- name: Pull LFS objects in submodules
	run: git submodule foreach --recursive 'git lfs pull'

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.12'

	- name: Add Conda to system path
	run: echo "$CONDA/bin" >> $GITHUB_PATH

	- name: Install dependencies
	run: conda install -c conda-forge mamba

	- name: Setup Snakemake
	run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http

	- name: List options of workflow
	run: \|
	snakemake --cores 1 --config list_commands=True --verbose --debug

	- name: Run workflow
	run: \|
	snakemake --cores 1 --software-deployment-method conda --config reference=T2T use_light_data=True chromosomes=[chr17] \
	--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

	Testing-with-mm10:
	runs-on: ubuntu-latest
	needs:
	- Formatting
	- Linting
	- Testing-basic
	- Testing-basic-with-slurm
	steps:
	- name: Checkout repository with submodules and LFS
	uses: actions/checkout@v4
	with:
	submodules: recursive
	lfs: true

	- name: Pull LFS objects in submodules
	run: git submodule foreach --recursive 'git lfs pull'

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.12'

	- name: Add Conda to system path
	run: echo "$CONDA/bin" >> $GITHUB_PATH

	- name: Install dependencies
	run: conda install -c conda-forge mamba

	- name: Setup Snakemake
	run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http

	- name: List options of workflow
	run: \|
	snakemake --cores 1 --config list_commands=True --verbose --debug

	- name: Run workflow
	run: \|
	snakemake --cores 1 --software-deployment-method conda --config reference=T2T use_light_data=True chromosomes=[chr17] \
	--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile


	# Testing_publishdir:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config_ashleys.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config_ashleys.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba --report report.zip"

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Updating the different GH actions #53

Workflow file

Updating the different GH actions #53

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Workflow file for this run