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refactor: rewrite nf-tests to use assertAll and precise naming #57

refactor: rewrite nf-tests to use assertAll and precise naming

refactor: rewrite nf-tests to use assertAll and precise naming #57

Workflow file for this run

name: test
on:
push:
branches: [main]
paths-ignore:
- "!**/*.md"
pull_request:
branches: [main]
paths-ignore:
- "!**/*.md"
merge_group:
types: [checks_requested]
branches: [main]
# Cancel if a newer run is started
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
prettier:
runs-on: ubuntu-latest
steps:
- name: Check out repository
uses: actions/checkout@v3
- name: Install NodeJS
uses: actions/setup-node@v3
- name: Install Prettier
run: npm install -g prettier
- name: Run Prettier --check
run: prettier --check .
nf-test:
runs-on: ubuntu-20.04
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v3
- uses: actions/setup-java@v3
with:
distribution: "temurin"
java-version: "17"
- name: Cache software installation
id: cache-software
uses: actions/cache@v3
with:
path: |
/usr/local/bin/nextflow
/usr/local/bin/nf-test
/home/runner/.nf-test/nf-test.jar
key: ${{ runner.os }}-software-${{ github.workspace }}
- name: Install Nextflow
env:
CAPSULE_LOG: none
if: steps.cache-software.outputs.cache-hit != 'true'
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install nf-test
if: steps.cache-software.outputs.cache-hit != 'true'
run: |
wget -qO- https://code.askimed.com/install/nf-test | bash
sudo mv nf-test /usr/local/bin/
nf-test update-plugins
- name: Run pipeline and cache dependencies
run: |
nextflow run main.nf
# Test the module
- name: Run nf-test
run: |
java -version
nf-test test --tap=test.tap
- uses: pcolby/tap-summary@v1
with:
path: >-
test.tap