Fixed insert cli

databio · Nov 27, 2023 · fb99493 · fb99493
1 parent ad61770
commit fb99493
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Showing 3 changed files with 28 additions and 9 deletions.
diff --git a/bedboss/bedboss.py b/bedboss/bedboss.py
@@ -201,9 +201,12 @@ def insert_pep(
     just_db_commit: bool = False,
     no_db_commit: bool = False,
     force_overwrite: bool = False,
+    *args,
+    **kwargs,
 ) -> NoReturn:
     """
     Run all bedboss pipelines for all samples in the pep file.
+    bedmaker -> bedqc -> bedstat -> qdrant_indexing -> bedbuncher
 
     :param bedbase_config: bedbase configuration file path
     :param output_folder: output statistics folder
@@ -256,13 +259,17 @@ def insert_pep(
             just_db_commit=just_db_commit,
             no_db_commit=no_db_commit,
             force_overwrite=force_overwrite,
-            skip_qdrant=skip_qdrant
+            skip_qdrant=skip_qdrant,
         )
         pep.samples[i].record_identifier = bed_id
 
     if create_bedset:
         _LOGGER.info(f"Creating bedset from {pep.name}")
-        run_bedbuncher(bedbase_config=bedbase_config, bedset_pep=pep, pephub_registry_path=pephub_registry_path)
+        run_bedbuncher(
+            bedbase_config=bedbase_config,
+            bedset_pep=pep,
+            pephub_registry_path=pephub_registry_path,
+        )
     else:
         _LOGGER.info(
             f"Skipping bedset creation. Create_bedset is set to {create_bedset}"
@@ -297,7 +304,7 @@ def main(test_args: dict = None) -> NoReturn:
     if args_dict["command"] == "all":
         run_all(pm=pm, **args_dict)
     elif args_dict["command"] == "insert":
-        insert_pep(args_dict["pep_config"])
+        insert_pep(**args_dict)
     elif args_dict["command"] == "make":
         BedMaker(pm=pm, **args_dict)
     elif args_dict["command"] == "qc":

diff --git a/bedboss/bedbuncher/bedbuncher.py b/bedboss/bedbuncher/bedbuncher.py
@@ -203,6 +203,8 @@ def add_bedset_to_database(
         "pephub_path": pephub_registry_path or "",
     }
 
+    print(pephub_registry_path)
+
     if heavy:
         _LOGGER.info("Heavy processing is True. Calculating plots...")
         plot_value = create_plots(

diff --git a/bedboss/bedstat/bedstat.py b/bedboss/bedstat/bedstat.py
@@ -111,9 +111,17 @@ def bedstat(
     )
     if not just_db_commit:
         if not pm:
+            pm_out_path = os.path.abspath(
+                os.path.join(outfolder_stats, "pypiper", bed_digest)
+            )
+            try:
+                os.makedirs(pm_out_path)
+            except FileExistsError:
+                pass
             pm = pypiper.PipelineManager(
                 name="bedstat-pipeline",
-                outfolder=outfolder,
+                outfolder=pm_out_path,
+                pipestat_sample_name=bed_digest,
             )
 
         rscript_path = os.path.join(
@@ -148,11 +156,13 @@ def bedstat(
 
         if not other_metadata:
             other_metadata = {}
-        other_metadata.update({"description": description,
-                               "treatment": treatment,
-                               "cell_type": cell_type,
-                               })
-
+        other_metadata.update(
+            {
+                "description": description,
+                "treatment": treatment,
+                "cell_type": cell_type,
+            }
+        )
 
         # unlist the data, since the output of regionstat.R is a dict of lists of
         # length 1 and force keys to lower to correspond with the