diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 72b2736..8c7cf73 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -49,15 +49,15 @@ jobs: - name: lint snakemake files with snakemake --lint shell: bash -el {0} - run: cd test_example && snakemake -s ../Snakefile --lint && cd .. + run: cd test_example && snakemake --lint && cd .. - - name: run pipeline with default config + - name: run pipeline on test example shell: bash -el {0} run: > rm -rf docs && cd test_example && rm -rf results - && snakemake -s ../Snakefile -j 2 + && snakemake --use-conda -j 2 && cd .. - name: Upload log files in case of error diff --git a/README.md b/README.md index 432374a..285ad40 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ # `seqneut-pipeline` for analyzing sequencing-based neutralization assays +[![Build Status](https://github.com/jbloomlab/seqneut-pipeline/actions/workflows/test.yaml/badge.svg)](https://github.com/jbloomlab/seqneut-pipeline/actions/workflows/test.yaml) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)