Add RNA-Seq TIN QC support #247
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# This workflow will build and test LongReadSum | |
name: build tests | |
on: | |
push: | |
branches: [ main ] | |
pull_request: | |
branches: [ main ] | |
jobs: | |
build-and-test: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Download assets | |
uses: dsaltares/fetch-gh-release-asset@1.0.0 | |
with: | |
repo: 'WGLab/LongReadSum' | |
version: 'tags/v1.3.1' | |
file: 'SampleData.zip' | |
- name: Unzip assets | |
shell: bash --login {0} | |
run: unzip SampleData.zip | |
- name: Set up conda environment | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
activate-environment: longreadsum | |
environment-file: environment.yml | |
python-version: 3.9 | |
auto-activate-base: false | |
- name: Check conda environment activation | |
shell: bash --login {0} | |
run: | | |
conda info --envs | |
which python | |
python --version | |
- name: Build LongReadSum | |
shell: bash --login {0} # --login enables PATH variable access | |
run: | | |
conda activate longreadsum | |
make | |
- name: Run tests | |
shell: bash --login {0} | |
run: | | |
conda activate longreadsum | |
mkdir output # Unit test output folder | |
python -m pytest |