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chore/docs: Merged all dependencies into env.yaml. #48

chore/docs: Merged all dependencies into env.yaml.

chore/docs: Merged all dependencies into env.yaml. #48

Workflow file for this run

name: CI
on: [push, pull_request]
jobs:
test:
runs-on: ubuntu-latest
steps:
- name: Checkout directory.
uses: actions/checkout@v3
with:
lfs: 'true'
- name: Install Python.
uses: actions/setup-python@v5
with:
python-version: '3.12'
- name: Install Snakemake and testing dependencies.
run: |
pip install -r <(yq -r '.dependencies[] | select(type == "!!map") | to_entries[].value[]' test/env_dev.yaml)
- name: Install Singularity.
uses: singularityhub/install-singularity@main
- name: Test scripts.
run: |
pytest -vvv
- name: Test run chr8 and chr21 workflow.
run: |
snakemake -c 2 -p \
--sdm apptainer conda \
--configfile test/config/config.yaml \
--show-failed-logs \
--apptainer-args "--bind $HOME:$HOME"