From 29edc94c533839d6de933bd3e9d78e3e7de1b81d Mon Sep 17 00:00:00 2001 From: ptajvar Date: Mon, 15 Jun 2026 09:27:10 +0000 Subject: [PATCH 1/8] update pna_graph_refinement_stage_leiden_resolution and pna_graph_refinement_stage_max_edges_to_remove default values --- nextflow.config | 4 ++-- nextflow_schema.json | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow.config b/nextflow.config index aab39cd9..c629e24e 100644 --- a/nextflow.config +++ b/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 diff --git a/nextflow_schema.json b/nextflow_schema.json index 7ae7f5bc..9bffa215 100644 --- a/nextflow_schema.json +++ b/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." }, From dbadda3e8542ce9088f6bb80cb1fdd6c68c7e182 Mon Sep 17 00:00:00 2001 From: ptajvar Date: Mon, 15 Jun 2026 09:30:21 +0000 Subject: [PATCH 2/8] update CHANGELOG.md --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ba339f2d..ae95fd18 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,9 @@ 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 +- 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. + ## [[4.1.2](https://github.com/nf-core/pixelator/releases/tag/4.1.2)] - 2026-06-04 ### Enhancements & fixes From 234b74172f0b97faa4e10263af154917627418ed Mon Sep 17 00:00:00 2001 From: ptajvar Date: Mon, 15 Jun 2026 11:06:39 +0000 Subject: [PATCH 3/8] lower pna_graph_component_size_min_threshold for v2 test --- subworkflows/local/pna/v2/tests/main.nf.test | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/pna/v2/tests/main.nf.test b/subworkflows/local/pna/v2/tests/main.nf.test index 14f4ee69..668b035a 100644 --- a/subworkflows/local/pna/v2/tests/main.nf.test +++ b/subworkflows/local/pna/v2/tests/main.nf.test @@ -17,11 +17,12 @@ nextflow_workflow { skip_experiment_summary = true outdir = "$outputDir" pna_demux_output_chunk_reads = "30K" + pna_graph_component_size_min_threshold = 10 } workflow { """ - def meta = [ pool:'pool1', id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v1' ] + def meta = [ pool:'pool1', id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ] input[0] = Channel.of([ meta, [ From 873851e8c1e330f9a53945c9fa6d3659d5e45ff1 Mon Sep 17 00:00:00 2001 From: ptajvar Date: Mon, 15 Jun 2026 11:23:03 +0000 Subject: [PATCH 4/8] lower pna_graph_component_size_min_threshold for v2 test to 2 --- subworkflows/local/pna/v2/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/pna/v2/tests/main.nf.test b/subworkflows/local/pna/v2/tests/main.nf.test index 668b035a..f4003e08 100644 --- a/subworkflows/local/pna/v2/tests/main.nf.test +++ b/subworkflows/local/pna/v2/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { skip_experiment_summary = true outdir = "$outputDir" pna_demux_output_chunk_reads = "30K" - pna_graph_component_size_min_threshold = 10 + pna_graph_component_size_min_threshold = 2 } workflow { From cdaec15c4cc5aff9435de36cdfac96dfdbbc5644 Mon Sep 17 00:00:00 2001 From: ptajvar Date: Mon, 15 Jun 2026 11:34:36 +0000 Subject: [PATCH 5/8] set pna_graph_component_size_min_threshold to 10 for both v1 and v2 --- subworkflows/local/pna/v1/tests/main.nf.test | 1 + subworkflows/local/pna/v2/tests/main.nf.test | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/pna/v1/tests/main.nf.test b/subworkflows/local/pna/v1/tests/main.nf.test index 660477a1..d40bdecc 100644 --- a/subworkflows/local/pna/v1/tests/main.nf.test +++ b/subworkflows/local/pna/v1/tests/main.nf.test @@ -17,6 +17,7 @@ nextflow_workflow { skip_experiment_summary = true outdir = "$outputDir" pna_demux_output_chunk_reads = "30K" + pna_graph_component_size_min_threshold = 10 } workflow { diff --git a/subworkflows/local/pna/v2/tests/main.nf.test b/subworkflows/local/pna/v2/tests/main.nf.test index f4003e08..668b035a 100644 --- a/subworkflows/local/pna/v2/tests/main.nf.test +++ b/subworkflows/local/pna/v2/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { skip_experiment_summary = true outdir = "$outputDir" pna_demux_output_chunk_reads = "30K" - pna_graph_component_size_min_threshold = 2 + pna_graph_component_size_min_threshold = 10 } workflow { From 3ec7e58e66f60c66b5a9fd387975e130d34cdd64 Mon Sep 17 00:00:00 2001 From: ptajvar Date: Thu, 18 Jun 2026 06:35:37 +0000 Subject: [PATCH 6/8] set test pna_graph_component_size_min_threshold to 25 --- conf/test_proxiome_v1.config | 2 +- conf/test_proxiome_v2.config | 2 +- modules/local/pixelator/graph/tests/main.nf.test | 4 ++-- subworkflows/local/pna/v1/tests/main.nf.test | 1 - subworkflows/local/pna/v2/tests/main.nf.test | 1 - 5 files changed, 4 insertions(+), 6 deletions(-) diff --git a/conf/test_proxiome_v1.config b/conf/test_proxiome_v1.config index afe193a4..e015f0a0 100644 --- a/conf/test_proxiome_v1.config +++ b/conf/test_proxiome_v1.config @@ -19,7 +19,7 @@ params { input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v1.csv' input_basedir = params.pipelines_testdata_base_path + '/testdata/pna' - pna_graph_component_size_min_threshold = 100 + pna_graph_component_size_min_threshold = 25 skip_layout = false technology = "proxiome-v1" diff --git a/conf/test_proxiome_v2.config b/conf/test_proxiome_v2.config index 7273a4df..a410a877 100644 --- a/conf/test_proxiome_v2.config +++ b/conf/test_proxiome_v2.config @@ -19,7 +19,7 @@ params { input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' input_basedir = params.pipelines_testdata_base_path + '/testdata/pna' - pna_graph_component_size_min_threshold = 100 + pna_graph_component_size_min_threshold = 25 skip_layout = false technology = "proxiome-v2" diff --git a/modules/local/pixelator/graph/tests/main.nf.test b/modules/local/pixelator/graph/tests/main.nf.test index 65f519bd..cdf61220 100644 --- a/modules/local/pixelator/graph/tests/main.nf.test +++ b/modules/local/pixelator/graph/tests/main.nf.test @@ -13,7 +13,7 @@ nextflow_process { when { params { - pna_graph_component_size_min_threshold = 100 + pna_graph_component_size_min_threshold = 25 } process { @@ -39,7 +39,7 @@ nextflow_process { test("PNA graph - small test") { when { params { - pna_graph_component_size_min_threshold = 100 + pna_graph_component_size_min_threshold = 25 outdir = "$outputDir" } diff --git a/subworkflows/local/pna/v1/tests/main.nf.test b/subworkflows/local/pna/v1/tests/main.nf.test index d40bdecc..660477a1 100644 --- a/subworkflows/local/pna/v1/tests/main.nf.test +++ b/subworkflows/local/pna/v1/tests/main.nf.test @@ -17,7 +17,6 @@ nextflow_workflow { skip_experiment_summary = true outdir = "$outputDir" pna_demux_output_chunk_reads = "30K" - pna_graph_component_size_min_threshold = 10 } workflow { diff --git a/subworkflows/local/pna/v2/tests/main.nf.test b/subworkflows/local/pna/v2/tests/main.nf.test index 668b035a..fb923470 100644 --- a/subworkflows/local/pna/v2/tests/main.nf.test +++ b/subworkflows/local/pna/v2/tests/main.nf.test @@ -17,7 +17,6 @@ nextflow_workflow { skip_experiment_summary = true outdir = "$outputDir" pna_demux_output_chunk_reads = "30K" - pna_graph_component_size_min_threshold = 10 } workflow { From 43edcd250091b8f3ca166e4b55f9c3f0c8f80ac8 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 15 Jun 2026 16:34:16 +0200 Subject: [PATCH 7/8] Update pixelatorES to 0.11.2 --- modules/local/experiment_summary/main.nf | 4 ++-- modules/local/experiment_summary/tests/main.nf.test.snap | 6 +++--- tests/proxiome_v1.nf.test.snap | 6 +++--- tests/proxiome_v2.nf.test.snap | 6 +++--- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/modules/local/experiment_summary/main.nf b/modules/local/experiment_summary/main.nf index 6cc5053e..ff2bb9d0 100644 --- a/modules/local/experiment_summary/main.nf +++ b/modules/local/experiment_summary/main.nf @@ -4,8 +4,8 @@ process EXPERIMENT_SUMMARY { label "error_retry" container "${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 diff --git a/modules/local/experiment_summary/tests/main.nf.test.snap b/modules/local/experiment_summary/tests/main.nf.test.snap index 41f08551..34bda7d6 100644 --- a/modules/local/experiment_summary/tests/main.nf.test.snap +++ b/modules/local/experiment_summary/tests/main.nf.test.snap @@ -11,7 +11,7 @@ [ "EXPERIMENT_SUMMARY", "experiment-summary", - "0.10.4 " + "0.11.2 " ] ] ], @@ -27,7 +27,7 @@ [ "EXPERIMENT_SUMMARY", "experiment-summary", - "0.10.4 " + "0.11.2 " ] ] ], @@ -37,4 +37,4 @@ "nextflow": "25.10.5" } } -} \ No newline at end of file +} diff --git a/tests/proxiome_v1.nf.test.snap b/tests/proxiome_v1.nf.test.snap index 1e0582d3..b52e0d57 100644 --- a/tests/proxiome_v1.nf.test.snap +++ b/tests/proxiome_v1.nf.test.snap @@ -114,7 +114,7 @@ "cat": 9.5 }, "EXPERIMENT_SUMMARY": { - "experiment-summary": "0.10.4" + "experiment-summary": "0.11.2" }, "PIXELATOR_AMPLICON": { "pixelator": "0.28.0" @@ -162,7 +162,7 @@ "cat": 9.5 }, "EXPERIMENT_SUMMARY": { - "experiment-summary": "0.10.4" + "experiment-summary": "0.11.2" }, "PIXELATOR_AMPLICON": { "pixelator": "0.28.0" @@ -307,4 +307,4 @@ "nextflow": "25.10.5" } } -} \ No newline at end of file +} diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap index 1c655374..04d58b70 100644 --- a/tests/proxiome_v2.nf.test.snap +++ b/tests/proxiome_v2.nf.test.snap @@ -151,7 +151,7 @@ "cat": 9.5 }, "EXPERIMENT_SUMMARY": { - "experiment-summary": "0.10.4" + "experiment-summary": "0.11.2" }, "PIXELATOR_AMPLICON": { "pixelator": "0.28.0" @@ -199,7 +199,7 @@ "cat": 9.5 }, "EXPERIMENT_SUMMARY": { - "experiment-summary": "0.10.4" + "experiment-summary": "0.11.2" }, "PIXELATOR_AMPLICON": { "pixelator": "0.28.0" @@ -395,4 +395,4 @@ "nextflow": "25.10.5" } } -} \ No newline at end of file +} From 72252681b7c334869bcd61b44969aff0e8779dc9 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 22 Jun 2026 16:00:49 +0200 Subject: [PATCH 8/8] Roll back graph parameters for test profile --- conf/test_proxiome_v1.config | 4 +++- conf/test_proxiome_v2.config | 4 +++- modules/local/pixelator/graph/tests/main.nf.test | 8 +++----- tests/proxiome_v1.nf.test.snap | 10 +++++----- tests/proxiome_v2.nf.test.snap | 10 +++++----- 5 files changed, 19 insertions(+), 17 deletions(-) diff --git a/conf/test_proxiome_v1.config b/conf/test_proxiome_v1.config index 2b9fcd5b..ef029529 100644 --- a/conf/test_proxiome_v1.config +++ b/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 = 25 + // 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. diff --git a/conf/test_proxiome_v2.config b/conf/test_proxiome_v2.config index 436e85d3..35af3a70 100644 --- a/conf/test_proxiome_v2.config +++ b/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 = 25 + // 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. diff --git a/modules/local/pixelator/graph/tests/main.nf.test b/modules/local/pixelator/graph/tests/main.nf.test index 3588a6e9..99f1b03b 100644 --- a/modules/local/pixelator/graph/tests/main.nf.test +++ b/modules/local/pixelator/graph/tests/main.nf.test @@ -12,10 +12,6 @@ nextflow_process { options "-stub" when { - params { - pna_graph_component_size_min_threshold = 25 - } - process { """ input[0] = [ @@ -39,7 +35,9 @@ nextflow_process { test("PNA graph - small test") { when { params { - pna_graph_component_size_min_threshold = 25 + // 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" } diff --git a/tests/proxiome_v1.nf.test.snap b/tests/proxiome_v1.nf.test.snap index 5d63b110..7ec2210f 100644 --- a/tests/proxiome_v1.nf.test.snap +++ b/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" } } -} +} \ No newline at end of file diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap index b2ef0e26..6a5e7533 100644 --- a/tests/proxiome_v2.nf.test.snap +++ b/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" } } -} +} \ No newline at end of file