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Merge pull request #58 from friendsofstrandseq/weber8thomas/fix-common #93

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Merge pull request #58 from friendsofstrandseq/weber8thomas/fix-common

Merge pull request #58 from friendsofstrandseq/weber8thomas/fix-common #93

Workflow file for this run

.github/workflows/main_test.yaml at 522f998
name: ashleys-qc-pipeline workflow checks
on:
push:
branches:
- "**"
jobs:
Formatting:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/[email protected]
- 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/[email protected]
- 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 >> $GITHUB_PATH
- name: Install dependencies
run: |
conda install -c conda-forge mamba
- name: Setup snakemake
run: |
mamba install -c conda-forge -c bioconda snakemake==7.32.4
- name: Run Snakemake Lint
run: |
snakemake --config data_location=github-actions-runner/.tests-mock/data_CHR17 --lint
Testing-basic:
runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
steps:
- name: Checkout repository with submodules
uses: actions/[email protected]
with:
submodules: recursive
# Update references
- name: Git Submodule Update
run: |
git pull --recurse-submodules
git submodule update --remote --recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: List contents of .tests
run: |
tree -h .tests
- name: Show config file
run: |
cat .tests/config/simple_config_ashleys.yaml
- name: List contents of workflow/data
run: |
tree -h workflow/data
- name: Add Conda to system path
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install dependencies
run: conda install -c conda-forge mamba
- name: Setup Snakemake
run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_ashleys.yaml \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
# Testing-basic-with-slurm:
# runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
# - Testing-basic
# services:
# mysql:
# image: mysql:8.0
# env:
# MYSQL_ROOT_PASSWORD: root
# ports:
# - "8888:3306"
# options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
# steps:
# - uses: actions/checkout@v3
# - uses: koesterlab/setup-slurm-action@v1
# - name: Checkout repository with submodules and LFS
# uses: actions/[email protected]
# with:
# submodules: recursive
# lfs: true
# - name: Pull LFS objects in submodules
# run: git submodule foreach --recursive 'git lfs pull'
# - name: List contents of .tests
# run: |
# tree -h .tests
# - name: List contents of workflow/data
# run: |
# tree -h workflow/data
# - name: Setup Python
# uses: actions/setup-python@v5
# with:
# python-version: '3.12'
# - name: Add Conda to system path
# run: echo "$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==7.32.4
# - name: Run workflow on SLURM
# run: |
# snakemake -j 1 -c 1 --executor slurm --workflow-profile .tests/config/slurm_config/ \
# --use-conda --conda-frontend mamba --configfile .tests/config/simple_config_ashleys.yaml -p --snakefile workflow/Snakefile