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Add CI/CD for using dockerfile for wdl
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kheal committed Nov 15, 2024
1 parent a169b58 commit f5ec2e8
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39 changes: 39 additions & 0 deletions .github/workflows/dockerfile_build.yml
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name: MiniWDL linter CI Dev DockerFile

on:
push:
workflow_dispatch:

jobs:
run-miniwdl:
runs-on: ubuntu-latest

steps:
- name: Checkout repository
uses: actions/checkout@v2

- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: '3.8' # specify the Python version you need

- name: Install Docker
run: |
sudo apt-get update
sudo apt-get install -y docker.io
sudo systemctl start docker
sudo systemctl enable docker
sudo usermod -aG docker $USER
- name: Build Docker Image
run: |
docker build -t local-metams:latest .
- name: Install MiniWDL
run: |
python -m pip install --upgrade pip
pip install miniwdl
- name: Run MiniWDL
run: |
miniwdl run wdl/metaMS_lipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files

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