diff --git a/CHANGELOG.md b/CHANGELOG.md index 7d5f5bb4..0536f14a 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/conf/test_proxiome_v1.config b/conf/test_proxiome_v1.config index db87bac4..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 = 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. diff --git a/conf/test_proxiome_v2.config b/conf/test_proxiome_v2.config index 39812540..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 = 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. diff --git a/modules/local/experiment_summary/tests/main.nf.test.snap b/modules/local/experiment_summary/tests/main.nf.test.snap index 7e49a2a0..5c1ed3e8 100644 --- a/modules/local/experiment_summary/tests/main.nf.test.snap +++ b/modules/local/experiment_summary/tests/main.nf.test.snap @@ -37,4 +37,4 @@ "nextflow": "25.10.5" } } -} \ No newline at end of file +} diff --git a/modules/local/pixelator/graph/tests/main.nf.test b/modules/local/pixelator/graph/tests/main.nf.test index d5a1f59b..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 = 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" } diff --git a/nextflow.config b/nextflow.config index 53501772..a508eb40 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 2ae1b828..963d971f 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." }, diff --git a/tests/proxiome_v1.nf.test.snap b/tests/proxiome_v1.nf.test.snap index c6e254b4..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 b50c7945..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