multiple changes:

- set up pipestatmanager based on pipelinemanager init args
- add pipestat argument group

pypiper/manager.py

@@ -108,7 +108,8 @@ def __init__(
             dirty=False, recover=False, new_start=False, force_follow=False,
             cores=1, mem="1000M", config_file=None, output_parent=None,
             overwrite_checkpoints=False, logger_kwargs=None,
-            pipestat_manager=None, **kwargs
+            pipestat_namespace=None, pipestat_record_id=None, pipestat_schema=None,
+            pipestat_results_file=None, pipestat_config=None, **kwargs
     ):
 
         # Params defines the set of options that could be updated via
@@ -347,7 +348,16 @@ def __init__(
             self.debug("No config file")
             self.config = None
 
-        self._pipestat_manager = pipestat_manager
+        # pipesatat setup
+        potential_namespace = getattr(self, "sample_name", self.name)
+        self._pipestat_manager = PipestatManager(
+            namespace=pipestat_namespace or potential_namespace,
+            record_identifier=pipestat_record_id or potential_namespace,
+            schema_path=pipestat_schema,
+            results_file_path=pipestat_results_file or pipeline_filepath(
+                self, filename="pipestat_results.yaml"),
+            config=pipestat_config
+        )
 
     @property
     def pipestat(self):

pypiper/utils.py

@@ -816,7 +816,10 @@ def _determine_args(argument_groups, arguments, use_all_args=False):
         "looper": ["config", "output-parent", "mem", "cores"],
         "common": ["input", "sample-name"],
         "ngs": ["sample-name", "input", "input2", "genome", "single-or-paired"],
-        "logmuse": LOGGING_CLI_OPTDATA.keys()
+        "logmuse": LOGGING_CLI_OPTDATA.keys(),
+        "pipestat": ["pipestat-namespace", "pipestat-record-id",
+                     "pipestat-schema", "pipestat-results-file",
+                     "pipestat-config"]
     }
 
     # Handle various types of group specifications.
@@ -936,7 +939,20 @@ def _add_args(parser, args, required):
                     "help": "Identifier for genome assembly"}),
         "single-or-paired":
             ("-Q", {"default": "single",
-                    "help": "Single- or paired-end sequencing protocol"})
+                    "help": "Single- or paired-end sequencing protocol"}),
+        "pipestat-namespace":
+            {"help": "Namespace to report into. This will be the DB table name "
+                     "if using DB as the object back-end"},
+        "pipestat-record-id":
+            {"help": "Record identifier to report for"},
+        "pipestat-schema":
+            {"help": "Path to the output schema that formalizes the "
+                     "results structure"},
+        "pipestat-config":
+            {"help": "Path to the configuration file"},
+        "pipestat-results-file":
+            {"help": "YAML file to report into, if file is used as "
+                     "the object back-end"}
     }
 
     from logmuse import LOGGING_CLI_OPTDATA