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name: "MultiQC - Windows"
on: [push, pull_request]
jobs:
run_multiqc:
name: Windows - Python ${{ matrix.python-version }}
runs-on: windows-latest
strategy:
matrix:
python-version: [2.7, 3.6, 3.7]
steps:
# Check out MultiQC code
- uses: actions/checkout@v1
# Set up Windows with C++ for numpy
- name: Visual Studio Command Prompt tool
run: cmd "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" ${{ matrix.platform-vcvars }}
# Set up Python
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python-version }}
# Install MultiQC
- name: Install MultiQC
run: python setup.py install
# Fetch the MultiQC test data
# NB: Download zip file instead of git clone, as Windows complains about reserved filenames and certain characters
- name: Download test data
run: |
curl -fsSL https://github.com/ewels/MultiQC_TestData/archive/master.zip -o test_data.zip
7z x test_data.zip -y -o"test_data"
dir test_data\MultiQC_TestData-master
# Run all of the tests! Remember the BACKslash path separator!
- name: Special case input data
run: multiqc test_data\MultiQC_TestData-master\data --ignore test_data\MultiQC_TestData-master\data\modules\
- name: All modules / Custom report filename
run: multiqc --lint test_data\MultiQC_TestData-master\data\modules\ --filename full_report.html
- name: File-list input of dirs
run: |
cd test_data\MultiQC_TestData-master
multiqc --file-list data\special_cases\dir_list.txt
- name: Specific module / Force overwrite / Prepend dirnames / Name and comment / No data dir
run: multiqc --lint test_data\MultiQC_TestData-master\data\modules\ -m fastqc -f -d -dd 1 -i "Forced Report" -b "This command has lots of options" --filename custom_fn --no-data-dir
- name: For overwrite / Flat plots / Tagged modules only / Exclude module / Ignore samples / Full names / zip data dir / config file
run: multiqc --lint test_data\MultiQC_TestData-master\data\modules\ -f --flat --tag methylation --exclude clusterflow --ignore-samples ngi --fullnames --zip-data-dir -c test\config_example.yaml
- name: Specfic module / named output dir / dev template / JSON data / File list
run: |
cd test_data\MultiQC_TestData-master
multiqc -m star -o testsmultiqc_report_dev -t default_dev -k json --file-list data\special_cases\file_list.txt
- name: Empty directory
run: |
mkdir empty_dir
multiqc -f empty_dir
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