update tests

.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

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)