Update github action for testing #11

Workflow file for this run

.github/workflows/main_test.yaml at 9a53ccb

	name: ashleys-qc-pipeline workflow checks

	on:
	push:
	branches:
	- "**"

	jobs:
	# WORK
	Formatting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4

	- name: Formatting
	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:
	- uses: actions/checkout@v4
	- name: Linting
	uses: snakemake/[email protected]
	with:
	directory: .
	snakefile: ./workflow/Snakefile
	args: "--lint --config ashleys_pipeline=True"
	Testing_ashleys:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Testing data
	uses: snakemake/[email protected]
	with:
	directory: .
	snakefile: ./workflow/Snakefile
	stagein: "conda config --set channel_priority flexible"
	args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug"
	- name: Testing report
	uses: snakemake/[email protected]
	with:
	directory: .
	snakefile: ./workflow/Snakefile
	args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba --report report.zip"
	Testing_ashleys_with_custom_python:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository with submodules
	uses: actions/checkout@v3
	with:
	submodules: recursive
	lfs: true
	- name: Setup Python
	uses: actions/setup-python@v2
	- 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==7.32.4"
	- name: Run workflow
	run: \|
	snakemake --cores 1 --use-conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

	Testing_ashleys_with_custom_python_singularity:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository with submodules
	uses: actions/checkout@v3
	with:
	submodules: recursive
	lfs: true
	- name: Setup Python
	uses: actions/setup-python@v2
	- 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==7.32.4" singularity
	- name: Run workflow
	run: \|
	snakemake --cores 1 --use-conda --use-singularity --configfile .tests/config/simple_config.yaml -p --verbose --debug --snakefile workflow/Snakefile

	# Testing_ashleys_fastqc_enabled:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config MultiQC=True --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config MultiQC=True --conda-frontend mamba --report report.zip"

	# Testing_ashleys_ms_norm_enabled:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config multistep_normalisation=True --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config multistep_normalisation=True --conda-frontend mamba --report report.zip"
	# Testing_ashleys_hg38:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
	# Testing_ashleys_hg19:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
	# Testing_ashleys_T2T:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
	# Testing_ashleys_mm10:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --config reference=mm10 use_light_data=True chromosomes=[chr17] --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --config reference=mm10 use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
	# Testing_jub_nb:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config hand_selection=True --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config hand_selection=True --conda-frontend mamba --report report.zip"
	# Testing_publishdir:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba --report report.zip"
	# Testing_list_commands:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/[email protected]
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --config list_commands=True --verbose --debug"

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Update github action for testing #11

Workflow file

Update github action for testing #11

Jobs

Run details

Workflow file for this run