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add workflow
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rachadele committed Jan 16, 2025
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38 changes: 38 additions & 0 deletions .github/workflows/build.yml
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name: Nextflow Pipeline Check

on:
push:
branches:
- main
pull_request:
branches:
- main

jobs:
check-nextflow:
runs-on: ubuntu-latest

steps:
# Step 1: Checkout the repository
- name: Checkout code
uses: actions/checkout@v3

# Step 2: Install Nextflow
- name: Install Nextflow
run: |
if ! command -v nextflow &> /dev/null; then
echo "Nextflow not found, installing..."
curl -s https://get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
else
echo "Nextflow already installed"
fi
# Step 3: Validate the Nextflow pipeline
- name: Validate pipeline syntax
run: nextflow -validate

# Step 4: Run the pipeline
- name: Run pipeline
run: |
nextflow run main.nf -profile conda -params-file params.mm.json

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