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MosaiCatcher basic checks

MosaiCatcher basic checks #577

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MosaiCatcher basic checks

MosaiCatcher basic checks #577

Workflow file for this run

.github/workflows/main.yaml at 2b6921d
name: MosaiCatcher basic checks
on:
push:
branches:
- "**"
schedule:
- cron: "0 0 * * 0"
jobs:
Formatting:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4.1.7
- 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 without 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 pull origin main'
- name: List contents of .tests-mock
run: |
tree -h github-actions-runner/.tests-mock
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: |
echo $CONDA/bin >> $GITHUB_PATH
- name: Install dependencies
run: |
conda install -c conda-forge mamba
- name: Setup snakemake
run: |
mamba install -c conda-forge -c bioconda snakemake==7.32.4
- name: Run Snakemake Lint
run: |
snakemake --config data_location=github-actions-runner/.tests-mock/data_CHR17 --lint
Testing-basic-v7:
runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
steps:
- name: Checkout repository with submodules
uses: actions/checkout@v4
with:
submodules: recursive
# Update references
- name: Git Submodule Update
run: |
# git pull --recurse-submodules
git submodule update --remote --recursive --force --init
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: List contents of .tests
run: |
tree -h .tests
- name: Show config file
run: |
cat .tests/config/simple_config_mosaicatcher.yaml
- name: List contents of workflow/data
run: |
tree -h workflow/data
- name: Add Conda to system path
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install dependencies
run: conda install -c conda-forge mamba
- name: Setup Snakemake
run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-basic-with-ashleys:
runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
steps:
- name: Checkout repository with submodules
uses: actions/checkout@v4
with:
submodules: recursive
# lfs: true
- name: Git Submodule Update
run: |
# git pull --recurse-submodules
git submodule update --remote --recursive --force --init
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: List contents of .tests
run: |
tree -h .tests
- name: Show config file
run: |
cat .tests/config/simple_config_mosaicatcher.yaml
- name: List contents of workflow/data
run: |
tree -h workflow/data
- name: Add Conda to system path
run: echo "$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==7.32.4
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config ashleys_pipeline=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile