Default to 8000 UMIs as minimum component size

CHANGELOG.md

@@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## dev - xxxx-xx-xx
 
+### Changed
+
+- Set default pna_graph_component_size_min_threshold to 8000 instead of null (i.e. automatic).
+
 ### Removed
 
 - Support for MPX in the pipeline

nextflow.config

@@ -66,7 +66,7 @@ params {
     pna_graph_initial_stage_max_edges_to_remove_relative    = null
     pna_graph_refinement_stage_max_edges_to_remove_relative = null
     pna_graph_graph_min_component_size_to_prune             = 100
-    pna_graph_component_size_min_threshold                  = null
+    pna_graph_component_size_min_threshold                  = 8000
 
     // PNA denoise
     pna_denoise_run_one_core_graph_denoising                = true

nextflow_schema.json

@@ -279,7 +279,8 @@
                 "pna_graph_component_size_min_threshold": {
                     "type": "number",
                     "minimum": 1,
-                    "description": "Components with fewer nodes than this will be filtered from the output data. This is typically not needed. Setting this will disable the automatic size filtering."
+                    "default": 8000,
+                    "description": "Components with fewer nodes than this will be filtered from the output data. Set to null to enable automatic size filtering based on the data."
                 }
             }
         },