Update pixelator to 0.29.0

CHANGELOG.md

@@ -5,6 +5,29 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [[4.2.0dev](https://github.com/nf-core/pixelator/releases/tag/4.1.2dev)] - 2026-MM-DD
 
+### Changed
+
+- 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`
+
+### Enhancements & fixes
+
+- Update pixelator container to 0.29.0
+- Update pixelatorES to 0.11.2
+
+### Software dependencies
+
+| Dependency    | Old version | New version |
+| ------------- | ----------- | ----------- |
+| `pixelator`   | 0.28.0      | 0.29.0      |
+| `pixelatorES` | 0.10.4      | 0.11.2      |
+
+### Parameters
+
+| Old parameter                             | New parameter                             |
+| ----------------------------------------- | ----------------------------------------- |
+| `pna_sample_calling_confidence_threshold` | `pna_sample_calling_enrichment_threshold` |
+
 ## [[4.1.2](https://github.com/nf-core/pixelator/releases/tag/4.1.2)] - 2026-06-04
 
 ### Enhancements & fixes

conf/modules.pna.config

@@ -160,7 +160,7 @@ process {
             [
                 params.pna_sample_calling_remove_incompatible ? "--remove-incompatible" : '',
                 params.pna_sample_calling_save_undetermined ? "--save-undetermined" : '',
-                params.pna_sample_calling_confidence_threshold != null ? "--confidence-threshold ${params.pna_sample_calling_confidence_threshold}" : '',
+                params.pna_sample_calling_enrichment_threshold != null ? "--enrichment-threshold ${params.pna_sample_calling_enrichment_threshold}" : '',
             ].join(' ').trim()
         }
         publishDir = [

conf/test_proxiome_v1.config

@@ -17,10 +17,14 @@ params {
 
     // Input data
     input                                  = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v1.csv'
-    input_basedir                          = params.pipelines_testdata_base_path + '/testdata/pna'
+    input_basedir                          = params.pipelines_testdata_base_path + '/new-test-data/pna'
 
     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.
+    pna_layout_layout_algorithm            = "wpmds_3d"
+
     skip_layout                            = false
     technology                             = "proxiome-v1"
     save_all                               = true

conf/test_proxiome_v2.config

@@ -16,11 +16,15 @@ params {
     config_profile_description             = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    input                                  = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv'
-    input_basedir                          = params.pipelines_testdata_base_path + '/testdata/pna'
+    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 nf-core test datasets include components too small for
+    // coarsened_pmds_3d. Keep wpmds_3d in  test profiles.
+    pna_layout_layout_algorithm            = "wpmds_3d"
+
     skip_layout                            = false
     technology                             = "proxiome-v2"
     save_all                               = true

docs/output.md

@@ -151,9 +151,10 @@ This step uses the `pixelator single-cell-pna sample-calling` command. It takes
 the graph PXL file and the sample sheet as input and assigns each component to
 the most likely sample in pooled experiments.
 
-Components with assignment confidence below the selected threshold are marked
-as undetermined and can be saved to a separate output file. The resulting
-per-sample dehashed PXL files are then used as input for the analysis step.
+Components with sample enrichment below `pna_sample_calling_enrichment_threshold`
+(default 10.0) are marked as undetermined and can be saved to a separate output
+file. The resulting per-sample dehashed PXL files are then used as input for
+the analysis step.
 
 <details markdown="1">
 <summary>Output files</summary>

modules/local/experiment_summary/main.nf

@@ -4,8 +4,8 @@ process EXPERIMENT_SUMMARY {
     label "error_retry"
 
     container "${params.experiment_summary_container?: workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'quay.io/pixelgen-technologies/pixelatores:0.10.4'
-        : 'quay.io/pixelgen-technologies/pixelatores:0.10.4'}"
+        ? 'quay.io/pixelgen-technologies/pixelatores:0.11.2'
+        : 'quay.io/pixelgen-technologies/pixelatores:0.11.2'}"
 
     input:
     path samplesheet_path