change log

Author: qclayssen

bolt/logging_config.py

@@ -1,10 +1,14 @@
 import logging
 import sys
 import pathlib
+from datetime import datetime
 
-
-def setup_logging(output_dir, log_filename):
+def setup_logging(output_dir, script_name):
+    # Create a timestamp for the log file
+    timestamp = datetime.now().strftime('%Y%m%d_%H%M%S')
+    log_filename = f"{script_name}_{timestamp}.log"
     log_file = pathlib.Path(output_dir) / log_filename
+
     logging.basicConfig(
         level=logging.DEBUG,
         format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
@@ -14,4 +18,4 @@ def setup_logging(output_dir, log_filename):
         ]
     )
     logger = logging.getLogger(__name__)
-    logger.info("Logging setup complete")
+    logger.info("Logging setup complete")

bolt/workflows/smlv_somatic/filter.py

@@ -7,6 +7,7 @@
 
 from ... import util
 from ...common import constants
+from ...logging_config import setup_logging
 
 
 @click.command(name='filter')
@@ -26,6 +27,9 @@ def entry(ctx, **kwargs):
     output_dir = pathlib.Path(kwargs['output_dir'])
     output_dir.mkdir(mode=0o755, parents=True, exist_ok=True)
 
+    script_name = pathlib.Path(__file__).stem
+    setup_logging("logs", script_name)
+
     # Open input VCF and set required header entries for output
     in_fh = cyvcf2.VCF(kwargs['vcf_fp'])
     header_filters = (

bolt/workflows/smlv_somatic/report.py

@@ -51,9 +51,8 @@ def entry(ctx, **kwargs):
     output_dir = pathlib.Path(kwargs['output_dir'])
     output_dir.mkdir(mode=0o755, parents=True, exist_ok=True)
 
-    setup_logging(output_dir, "smlv_somatic_annotate.py")
-    logger = logging.getLogger(__name__)
-
+    script_name = pathlib.Path(__file__).stem
+    setup_logging("logs", script_name)
 
     # BCFtools stats
     bcftools_vcf_fp = bcftools_stats_prepare(kwargs['vcf_fp'], kwargs['tumor_name'], output_dir)