.

Author: DaanJansen94

setup.py

@@ -1,6 +1,8 @@
 from setuptools import setup, find_packages
+from pathlib import Path
 
-with open("README.md", "r", encoding="utf-8") as fh:
+readme_path = Path(__file__).resolve().parent / "README.md"
+with readme_path.open("r", encoding="utf-8") as fh:
     long_description = fh.read()
 
 setup(

virasign/virasign.py

@@ -6216,7 +6216,7 @@ def process_sample(sample_name, sample_fastq, database_fasta, output_dir, min_id
         confident_names = save_results(
             sample_name, None, None, all_stats, filtered_stats, curated_stats,
             sample_dir, database_fasta, sample_fastq, min_identity, min_mapped_reads,
-            coverage_depth_threshold, coverage_breadth_threshold, threads,
+            coverage_depth_threshold, coverage_breadth_threshold, min_nogr, threads,
             gzip_fastq=gzip_fastq,
             minimap2_I=minimap2_I,
             blinded_species=blinded_species,