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Issue 396 - Migrate to ClinVar XML V2 #352

Issue 396 - Migrate to ClinVar XML V2

Issue 396 - Migrate to ClinVar XML V2 #352

Workflow file for this run

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
name: CMAT pipelines
on:
pull_request:
branches: [ master ]
workflow_dispatch:
jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.8
uses: actions/setup-python@v2
with:
python-version: 3.8
- name: Install native packages
run: |
sudo apt update
sudo apt -y install samtools bcftools parallel libbz2-dev liblzma-dev
- name: Install dependencies
run: |
python -m pip install --upgrade pip
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
python setup.py install
- name: Install Nextflow
run: |
mkdir /tmp/nextflow && cd /tmp/nextflow
wget -qO- get.nextflow.io | bash
echo "/tmp/nextflow" >> $GITHUB_PATH
cd -
- name: Unit tests
run: python -m pytest --cov=cmat -k "not integration"
- name: Integration tests
run: python -m pytest --cov=cmat --cov-append tests -k integration
- name: End-to-end test of evidence string generation pipeline
run: bash tests/pipelines/test_annotation_pipeline.sh
# TODO Takes too long to run regularly, maybe just on tags?
# - name: End-to-end test of curation pipelines
# run: bash tests/pipelines/test_curation_pipelines.sh
- name: Upload the coverage data to Coveralls
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: coveralls