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tests: create seperate dry run for CPU and GPU mode
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padraicc committed Apr 16, 2024
1 parent a291999 commit ba698b3
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33 changes: 33 additions & 0 deletions .github/workflows/snakemake-dry-run_cpu.yaml
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name: Snakemake dry run

on:
push:
branches:
- develop
- main
pull_request:
branches:
- develop
- main
workflow_dispatch:

jobs:
snakemake-dry-run:
name: Run snakemake dry run
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.9
uses: actions/setup-python@v3
with:
python-version: 3.9
- name: Install requirements.txt
run: |
pip install -r requirements.txt
- name: Install requirements.test.txt
run: |
pip install -r requirements.test.txt
- name: snakemake dry run
working-directory: .tests/integration
run: |
snakemake -n -s ../../workflow/Snakefile --configfile config/config.yaml --config aligner=bwa_cpu --config snp_caller=deepvariant_cpu
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