update pna_graph_refinement_stage_leiden_resolution and pna_graph_ref…

CHANGELOG.md

@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Rename `pna_sample_calling_confidence_threshold` to `pna_sample_calling_enrichment_threshold` to match pixelator 0.29.0
 - Change default layout algorithm from `wpmds_3d` to `coarsened_pmds_3d`
+- Change `pna_graph_refinement_stage_leiden_resolution` and `pna_graph_refinement_stage_max_edges_to_remove` default values
+  to 0.5, and 20 respectively based on latest evaluations.
 
 ### Enhancements & fixes
 

conf/test_proxiome_v1.config

@@ -19,7 +19,9 @@ params {
     input                                  = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v1.csv'
     input_basedir                          = params.pipelines_testdata_base_path + '/new-test-data/pna'
 
-    pna_graph_component_size_min_threshold = 100
+    // Synthetic data was generated to pass with the test with lower than default resolution
+    pna_graph_refinement_stage_leiden_resolution = 0.01
+    pna_graph_component_size_min_threshold       = 100
 
     // Synthetic nf-core test datasets include components too small for
     // coarsened_pmds_3d. Keep wpmds_3d in test profiles.

conf/test_proxiome_v2.config

@@ -19,7 +19,9 @@ params {
     input                                  = params.pipelines_testdata_base_path + '/new-test-data/samplesheet/pna/samplesheet_proxiome_v2.csv'
     input_basedir                          = params.pipelines_testdata_base_path + '/new-test-data/pna'
 
-    pna_graph_component_size_min_threshold = 100
+    // Synthetic data was generated to pass with the test with lower than default resolution
+    pna_graph_refinement_stage_leiden_resolution = 0.01
+    pna_graph_component_size_min_threshold       = 100
 
     // Synthetic nf-core test datasets include components too small for
     // coarsened_pmds_3d. Keep wpmds_3d in  test profiles.

modules/local/experiment_summary/tests/main.nf.test.snap

@@ -37,4 +37,4 @@
             "nextflow": "25.10.5"
         }
     }
-}
+}

modules/local/pixelator/graph/tests/main.nf.test

@@ -12,10 +12,6 @@ nextflow_process {
         options "-stub"
 
         when {
-            params {
-                pna_graph_component_size_min_threshold = 100
-            }
-
             process {
                 """
                 input[0] = [
@@ -39,7 +35,9 @@ nextflow_process {
     test("PNA graph - small test") {
         when {
             params {
-                pna_graph_component_size_min_threshold = 100
+                // Synthetic data was generated to pass with the test with lower than default resolution
+                pna_graph_refinement_stage_leiden_resolution = 0.01
+                pna_graph_component_size_min_threshold       = 100
                 outdir   = "$outputDir"
             }
 

nextflow.config

@@ -61,12 +61,12 @@ params {
     // PNA graph
     pna_graph_multiplet_recovery                            = true
     pna_graph_initial_stage_leiden_resolution               = 1.0
-    pna_graph_refinement_stage_leiden_resolution            = 0.01
+    pna_graph_refinement_stage_leiden_resolution            = 0.5
     pna_graph_min_count                                     = 1
     pna_graph_max_refinement_recursion_depth                = 3
     pna_graph_edge_cycle_verification                       = true
     pna_graph_initial_stage_max_edges_to_remove             = 10
-    pna_graph_refinement_stage_max_edges_to_remove          = 10
+    pna_graph_refinement_stage_max_edges_to_remove          = 20
     pna_graph_initial_stage_max_edges_to_remove_relative    = null
     pna_graph_refinement_stage_max_edges_to_remove_relative = null
     pna_graph_component_size_min_threshold                  = 8000

nextflow_schema.json

@@ -225,7 +225,7 @@
                     "help": "This should typically be set higher than the refinement stage resolution."
                 },
                 "pna_graph_refinement_stage_leiden_resolution": {
-                    "default": 0.01,
+                    "default": 0.5,
                     "fa_icon": "fas fa-sliders-h",
                     "minimum": 0,
                     "type": "number",
@@ -265,7 +265,7 @@
                 "pna_graph_refinement_stage_max_edges_to_remove": {
                     "type": "integer",
                     "fa_icon": "fas fa-trash",
-                    "default": 10,
+                    "default": 20,
                     "minimum": 1,
                     "description": "The maximum number of edges to remove between components during the refinement stage (iteration > 0) of multiplet recovery."
                 },

tests/proxiome_v1.nf.test.snap

@@ -295,16 +295,16 @@
                 "sample_2.meta.json:md5,e0b756a91edb80e878baa6862b2c3c6d",
                 "sample_1.meta.json:md5,eb91c047c438beb4c746cf2acba39ab5",
                 "sample_2.meta.json:md5,eb91c047c438beb4c746cf2acba39ab5",
-                "sample_1.meta.json:md5,9499ef2af613d6fa5cba5c91a443c726",
-                "sample_2.meta.json:md5,d73dc0fcfaaac01957e4611c89ef3dec",
+                "sample_1.meta.json:md5,cdede47a0ae5b110c5b30598313f2645",
+                "sample_2.meta.json:md5,b77ef4e36914f958b87c11aa61f4c05f",
                 "sample_1.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3",
                 "sample_2.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3"
             ]
         ],
-        "timestamp": "2026-06-17T09:37:29.80236891",
+        "timestamp": "2026-06-22T15:49:11.767104778",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.5"
+            "nextflow": "26.04.2"
         }
     }
 }

tests/proxiome_v2.nf.test.snap

@@ -375,8 +375,8 @@
                 "pool2.meta.json:md5,236a76417f95f0c289a226753df41340",
                 "pool1.meta.json:md5,eb91c047c438beb4c746cf2acba39ab5",
                 "pool2.meta.json:md5,eb91c047c438beb4c746cf2acba39ab5",
-                "pool1.meta.json:md5,b65ff9e07a33b36fd4a2620d34cd8209",
-                "pool2.meta.json:md5,b65ff9e07a33b36fd4a2620d34cd8209",
+                "pool1.meta.json:md5,d76c0ee2adbe089a689f81ec205350dd",
+                "pool2.meta.json:md5,d76c0ee2adbe089a689f81ec205350dd",
                 "sample1.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3",
                 "sample2.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3",
                 "sample3.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3",
@@ -389,10 +389,10 @@
                 "sample4.meta.json:md5,1c94e4736d2cf4a7f1960e85872f21fa"
             ]
         ],
-        "timestamp": "2026-06-17T09:44:16.688012834",
+        "timestamp": "2026-06-22T15:23:00.769318806",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.5"
+            "nextflow": "26.04.2"
         }
     }
 }