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Test snake v8 on GH actions #16

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Test snake v8 on GH actions

Test snake v8 on GH actions #16

Workflow file for this run

.github/workflows/main_test.yaml at 396dace
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 --default-storage-provider http"
- 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 --default-storage-provider http --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"