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end-to-end.yml
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name: End-to-end MGS workflow test
on:
pull_request:
branches:
- master
- dev
jobs:
test-index:
runs-on: ubuntu-latest
timeout-minutes: 10
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
test-run:
runs-on: ubuntu-latest
timeout-minutes: 10
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 run workflow
run: nf-test test --tag run --verbose
test-run-output:
runs-on: ubuntu-latest
timeout-minutes: 10
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 run workflow
run: nf-test test --tag run_output --verbose
test-validation:
runs-on: ubuntu-latest
timeout-minutes: 5
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 run_validation workflow
run: nf-test test --tag validation --verbose