fix loging path and redundancy

Author: qclayssen

bolt/workflows/smlv_somatic/annotate.py

@@ -51,9 +51,6 @@ def entry(ctx, **kwargs):
 
     setup_logging(output_dir, "smlv_somatic.log")
 
-    # Create a logger instance
-    logger = logging.getLogger(__name__)
-
     # Set all FILTER="." to FILTER="PASS" as required by PURPLE
     filter_pass_fp = set_filter_pass(kwargs['vcf_fp'], kwargs['tumor_name'], output_dir)
 

bolt/workflows/smlv_somatic/report.py

@@ -52,7 +52,7 @@ def entry(ctx, **kwargs):
     output_dir.mkdir(mode=0o755, parents=True, exist_ok=True)
 
     script_name = pathlib.Path(__file__).stem
-    setup_logging("logs", script_name)
+    setup_logging(output_dir, script_name)
 
     # BCFtools stats
     bcftools_vcf_fp = bcftools_stats_prepare(kwargs['vcf_fp'], kwargs['tumor_name'], output_dir)