Add graph refinement options for pixelator 0.19

.nf-core.yml

@@ -1,6 +1,8 @@
 bump_version: null
 lint:
   multiqc_config: false
+  files_unchanged:
+    - assets/nf-core-pixelator_logo_light.png
   files_exist:
     - assets/multiqc_config.yml
     - conf/igenomes.config

CHANGELOG.md

@@ -3,20 +3,44 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.4.0](https://github.com/nf-core/pixelator/releases/tag/1.4.0] - ????-??-??
+## [[1.4.0dev](https://github.com/nf-core/pixelator/releases/tag/1.4.0] - ????-??-??
 
 ### Enhancements & fixes
 
 - [[PR #111](https://github.com/nf-core/pixelator/pull/111)] - Template update for nf-core/tools v3.0.2
+- [[PR #112](https://github.com/nf-core/pixelator/pull/112)] - Add graph refinement options for pixelator 0.19
 
-## [[1.3.1](https://github.com/nf-core/pixelator/releases/tag/1.3.1)] - 2024-07-31
+### Parameters
+
+| Old parameter                        | New parameter                            |
+| ------------------------------------ | ---------------------------------------- |
+|                                      | `--help_full`                            |
+|                                      | `--show_hidden`                          |
+| `--validationFailUnrecognisedParams` |                                          |
+| `--validationLenientMode`            |                                          |
+| `--validationSchemaIgnoreParams`     |                                          |
+| `--validationShowHiddenParams`       |                                          |
+| `--leiden_iterations`                | `--graph_max_refinement_recursion_depth` |
+|                                      | `--graph_max_edges_to_split`             |
+
+> [!NOTE]
+> Parameter has been **updated** if both old and new parameter information is present.
+> Parameter has been **added** if just the new parameter information is present.
+> Parameter has been **removed** if new parameter information isn't present.
 
 ### Software dependencies
 
 | Dependency  | Old version | New version |
 | ----------- | ----------- | ----------- |
 | `pixelator` | 0.18.2      | 0.19.0      |
 
+> [!NOTE]
+> Dependency has been **updated** if both old and new parameter information is present.
+> Dependency has been **added** if just the new parameter information is present.
+> Dependency has been **removed** if new parameter information isn't present.
+
+## [[1.3.1](https://github.com/nf-core/pixelator/releases/tag/1.3.1)] - 2024-07-31
+
 ### Enhancements & fixes
 
 - [[PR #107](https://github.com/nf-core/pixelator/pull/107)] - Fix conda version tag to use pixelator 0.18.2

conf/modules.config

@@ -193,7 +193,6 @@ process {
                 params.max_neighbours ? "--max-neighbours ${params.max_neighbours}": '',
                 params.collapse_mismatches ? "--mismatches ${params.collapse_mismatches}": '',
                 params.collapse_min_count ? "--min-count ${params.collapse_min_count}": '',
-                params.collapse_use_counts ? "--use-counts": '',
             ].join(' ').trim()
         }
 
@@ -222,8 +221,9 @@ process {
         ext.args = {
             [
                 params.multiplet_recovery ? "--multiplet-recovery" : '',
-                params.leiden_iterations ? "--leiden-iterations ${params.leiden_iterations}" : '',
                 params.graph_min_count ? "--min-count ${params.graph_min_count}" : '',
+                params.graph_max_refinement_recursion_depth ? "--max-refinement-recursion-depth ${params.graph_max_refinement_recursion_depth}" : '',
+                params.graph_max_edges_to_split ? "--max-edges-to-split ${params.graph_max_edges_to_split}" : '',
             ].join(' ').trim()
         }
 

nextflow.config

@@ -37,12 +37,12 @@ params {
     max_neighbours          = 60
     collapse_mismatches     = 2
     collapse_min_count      = 2
-    collapse_use_counts     = false
 
     // graph options
-    multiplet_recovery      = true
-    leiden_iterations       = 10
-    graph_min_count         = 2
+    multiplet_recovery                   = true
+    graph_max_refinement_recursion_depth = 5
+    graph_max_edges_to_split             = 5
+    graph_min_count                      = 2
 
     // annotate options
     min_size                = null
@@ -87,7 +87,8 @@ params {
     skip_layout                        = false
 
     // Main pixelator container override
-    pixelator_container                =  null
+    // TODO: Remove this once the pixelator 0.19 is out
+    pixelator_container                = "ghcr.io/pixelgentechnologies/pixelator:dev"
 
     // Boilerplate options
     outdir                       = null

nextflow_schema.json

@@ -210,10 +210,6 @@
                     "minimum": 1,
                     "type": "integer"
                 },
-                "collapse_use_counts": {
-                    "description": "Use counts when collapsing (the difference in counts between two molecules must be more than double in order to be collapsed)",
-                    "type": "boolean"
-                },
                 "save_collapsed_reads": {
                     "fa_icon": "fas fa-save",
                     "type": "boolean",
@@ -232,13 +228,22 @@
                     "type": "boolean",
                     "default": true
                 },
-                "leiden_iterations": {
-                    "fa_icon": "fas repeat",
-                    "description": "Number of iterations for the leiden algorithm, high values will decrease the variance of the results but increase the runtime [default: 10; 1<=x<=100]",
+                "graph_max_refinement_recursion_depth": {
+                    "fa_icon": "fas less-than-equal",
+                    "description": "The number of times a component can be broken down into smaller components during the multiplet recovery process.",
                     "type": "integer",
+                    "default": 5,
                     "minimum": 1,
                     "maximum": 100,
-                    "default": 10,
+                    "hidden": true
+                },
+                "graph_max_edges_to_split": {
+                    "fa_icon": "fas less-than-equal",
+                    "description": "Maximum number of edges between the produced components as a result of a component split operation during the multiplet recovery process.",
+                    "type": "integer",
+                    "default": 5,
+                    "minimum": 1,
+                    "maximum": 1000,
                     "hidden": true
                 },
                 "graph_min_count": {