Skip to content

bcftbx/mock: fix broken bases mask for platform 'novaseq' in MockIllu… #155

bcftbx/mock: fix broken bases mask for platform 'novaseq' in MockIllu…

bcftbx/mock: fix broken bases mask for platform 'novaseq' in MockIllu… #155

Workflow file for this run

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
name: Python CI
on: [ push, pull_request ]
jobs:
build:
# Switched from ubuntu-latest to ubuntu-20.04 as former
# doesn't support Python 3.6
runs-on: ubuntu-20.04
strategy:
fail-fast: false
matrix:
python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install flake8 pytest
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Lint with flake8
run: |
# stop the build if there are Python syntax errors or undefined names
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: Test bcftbx
run: |
python -m pip install .
pytest bcftbx
- name: Test illumina2cluster utilities
run: |
./bin/prep_sample_sheet.py -h
./bin/verify_paired.py -h
- name: Test solid2cluster utilities
run: |
./bin/analyse_solid_run.py -h
- name: Test RNA-seq utilities
run: |
examples/RNA-seq/test_bowtie_mapping_stats.sh
- name: Test ChIP-seq utilities
run: |
examples/ChIP-seq/test_make_macs_xls.sh
examples/ChIP-seq/test_make_macs2_xls.sh
- name: Test NGS-general utilities
run: |
examples/NGS-general/test_extract_reads.sh
./bin/manage_seqs.py -h
./bin/reorder_fasta.py -h
./bin/sam2soap.py -h
./bin/split_fastq.py -h
./bin/split_fasta.py -h
- name: Test microarray utilities
run: |
examples/microarray/test_annotate_probesets.sh
examples/microarray/test_best_exons.sh
examples/microarray/test_xrorthologs.sh
- name: Test md5checker utility
run: |
examples/utils/test_md5checker.sh