add logginf for task filter_mudata

panpipes/panpipes/pipeline_preprocess.py

@@ -15,6 +15,14 @@
 
 # import pandas as pd
 
+import logging
+L = logging.getLogger('panpipes')
+L.setLevel(logging.INFO)
+log_handler = logging.FileHandler("pipeline.log")
+formatter = logging.Formatter('%(asctime)s: %(levelname)s - %(message)s')
+log_handler.setFormatter(formatter)
+L.addHandler(log_handler)
+
 PARAMS = P.get_parameters(
     ["%s/pipeline.yml" % os.path.splitext(__file__)[0],
      "pipeline.yml"])
@@ -52,8 +60,16 @@ def filter_mudata(outfile):
             cmd += " --keep_barcodes %(filtering_keep_barcodes)s"
         if PARAMS['intersect_mods'] is not None:
             cmd += " --intersect_mods %(intersect_mods)s"
-        cmd += " > logs/filtering.log "
+        logfile = "logs/filtering.log"
+        cmd += f" >  {logfile}"
         job_kwargs["job_threads"] = PARAMS['resources_threads_low']
+        L.info(
+            "Task: 'filter_mudata'" + "\n" +
+            f"Input file(s): {unfiltered_obj}" + "\n" +
+            f"Output file(s): {outfile}" + "\n" +
+            f"Log file: {logfile}" + "\n" +
+            "In case of error, please refer to the log file(s) above for more information."
+        )
         P.run(cmd, **job_kwargs)
     else:
         try: