nf-core_modules/.github/workflows/fastqc.yml

name: fastqc
on:
  push:
    paths:
      - software/fastqc/**
      - .github/workflows/fastqc.yml
      - tests
  pull_request:
    paths:
      - software/fastqc/**
      - .github/workflows/fastqc.yml
      - tests

jobs:
  ci_test:
    runs-on: ubuntu-latest
    env:
      NXF_ANSI_LOG: false
    steps:

    - uses: actions/checkout@v2

    - name: Install Nextflow
      run: |
        export NXF_VER="20.07.1"
        wget -qO- get.nextflow.io | bash
        sudo mv nextflow /usr/local/bin/

    - name: Set up Python
      uses: actions/setup-python@v2
      with:
        python-version: "3.x"
    - name: Install dependencies
      run: python -m pip install --upgrade pip pytest-workflow

    # Test the module
    - run: pytest --tag fastqc --symlink
Update tests 2020-08-07 08:31:27 +00:00			`name: fastqc`
Refactor GitHub actions workflows 2019-12-05 14:44:10 +00:00			`on:`
update GitHub actions for Fastqc 2020-07-16 12:49:08 +00:00			`push:`
Workflows - trigger on change to workflow and test data too 2020-07-16 15:14:57 +00:00			`paths:`
			`- software/fastqc/**`
			`- .github/workflows/fastqc.yml`
			`- tests`
Refactor GitHub actions workflows 2019-12-05 14:44:10 +00:00			`pull_request:`
Workflows - trigger on change to workflow and test data too 2020-07-16 15:14:57 +00:00			`paths:`
			`- software/fastqc/**`
			`- .github/workflows/fastqc.yml`
			`- tests`
Refactor GitHub actions workflows 2019-12-05 14:44:10 +00:00
			`jobs:`
Update tests 2020-08-07 08:31:27 +00:00			`ci_test:`
Refactor GitHub actions workflows 2019-12-05 14:44:10 +00:00			`runs-on: ubuntu-latest`
Fix up cutadapt tests 2020-07-11 15:14:14 +00:00			`env:`
			`NXF_ANSI_LOG: false`
Refactor GitHub actions workflows 2019-12-05 14:44:10 +00:00			`steps:`

Fix FastQC test 2020-07-17 08:43:50 +00:00			`- uses: actions/checkout@v2`
Refactor GitHub actions workflows 2019-12-05 14:44:10 +00:00
Actions: install nextflow 2019-12-05 15:03:00 +00:00			`- name: Install Nextflow`
			`run: \|`
Change NF version 2020-08-06 23:38:56 +00:00			`export NXF_VER="20.07.1"`
Actions: install nextflow 2019-12-05 15:03:00 +00:00			`wget -qO- get.nextflow.io \| bash`
			`sudo mv nextflow /usr/local/bin/`

ci(fastqc): Run pytest-workflow instead of workflow This will check for the actual output files and their contents not just whether the module runs or not. 2020-11-16 15:37:22 +00:00			`- name: Set up Python`
			`uses: actions/setup-python@v2`
			`with:`
			`python-version: "3.x"`
			`- name: Install dependencies`
			`run: python -m pip install --upgrade pip pytest-workflow`

Refactor GitHub actions workflows 2019-12-05 14:44:10 +00:00			`# Test the module`
ci(fastqc): Run pytest-workflow instead of workflow This will check for the actual output files and their contents not just whether the module runs or not. 2020-11-16 15:37:22 +00:00			`- run: pytest --tag fastqc --symlink`