From a9daeea6d51defcb40878644307a7688aa067aa4 Mon Sep 17 00:00:00 2001 From: ptajvar Date: Thu, 12 Feb 2026 09:51:21 +0100 Subject: [PATCH 1/2] default to 8000 UMIs as minimum component size --- nextflow.config | 2 +- nextflow_schema.json | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 5fbab318..d2e00257 100644 --- a/nextflow.config +++ b/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 diff --git a/nextflow_schema.json b/nextflow_schema.json index 5cf49f27..5e326fd8 100644 --- a/nextflow_schema.json +++ b/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." } } }, From 566a6d2facf480495f94ad2488b6f438ab1f1dae Mon Sep 17 00:00:00 2001 From: ptajvar Date: Thu, 12 Feb 2026 13:10:16 +0100 Subject: [PATCH 2/2] update CHANGELOG.md --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d4f9732c..dcc306e2 100644 --- a/CHANGELOG.md +++ b/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