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End-to-end MGS workflow test

Adding single-read functionality to RAW and CLEAN #63

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Adding single-read functionality to RAW and CLEAN

Adding single-read functionality to RAW and CLEAN #63

Workflow file for this run

.github/workflows/end-to-end.yml at e85dd45
name: End-to-end MGS workflow test
on: [pull_request]
jobs:
test:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Set up JDK 11
uses: actions/setup-java@v4
with:
java-version: '11'
distribution: 'adopt'
- name: Setup Nextflow latest (stable)
uses: nf-core/setup-nextflow@v1
with:
version: "latest"
- name: Install nf-test
run: |
wget -qO- https://get.nf-test.com | bash
sudo mv nf-test /usr/local/bin/
- name: Run index workflow
run: nf-test test --tag index --verbose
- name: Clean docker for more space
run: |
docker kill $(docker ps -q) 2>/dev/null || true
docker rm $(docker ps -a -q) 2>/dev/null || true
docker rmi $(docker images -q) -f 2>/dev/null || true
docker system prune -af --volumes
- name: Clean up nf-test dir
run: sudo rm -rf .nf-test
- name: Run run workflow
run: nf-test test --tag run --verbose
- name: Run run_validation workflow
run: nf-test test --tag validation --verbose