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Update README.md #49

Workflow file for this run

name: build
on:
push:
branches:
- main
- develop
pull_request:
branches:
- main
- develop
jobs:
build:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.9"]
steps:
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
cache: "pip"
- name: Install nextflow
uses: nf-core/setup-nextflow@v1
- name: Install dependencies
run: |
python -m pip install --upgrade pip setuptools
pip install .[dev,test]
python -c 'from logan.src.util import chmod_bins_exec; chmod_bins_exec()'
- name: Test stub run
run: |
mkdir tmp && cd tmp
which logan
logan init
logan run -profile ci_stub,docker \
--fastq_input "/opt2/.tests/*R{1,2}.fastq.gz" \
--vc --cnv --sv \
--genome hg38 \
--outdir /opt2/output_tn_fqs \
--interval /opt2/.tests/interval.bed \
-stub