Merge pull request #43 from friendsofstrandseq/dev #4

Workflow file for this run

.github/workflows/main_test.yaml at 33d8e87

	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/snakemake-github-action@v1.24.0
	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/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.yaml --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.yaml --conda-frontend mamba --report report.zip"

	Testing_ashleys_fastqc_enabled:
	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.yaml --config MultiQC=True --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.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/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.yaml --config multistep_normalisation=True --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.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/snakemake-github-action@v1.24.0
	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/snakemake-github-action@v1.24.0
	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/snakemake-github-action@v1.24.0
	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/snakemake-github-action@v1.24.0
	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/snakemake-github-action@v1.24.0
	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/snakemake-github-action@v1.24.0
	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/snakemake-github-action@v1.24.0
	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/snakemake-github-action@v1.24.0
	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/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.yaml --config hand_selection=True --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.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/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.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.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/snakemake-github-action@v1.24.0
	with:
	directory: .
	snakefile: ./workflow/Snakefile
	args: "--cores 1 --config list_commands=True --verbose --debug"

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Merge pull request #43 from friendsofstrandseq/dev #4

Workflow file

Merge pull request #43 from friendsofstrandseq/dev #4

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Workflow file for this run