update pna_graph_refinement_stage_leiden_resolution and pna_graph_ref… by ptajvar · Pull Request #226 · nf-core/pixelator

ptajvar · 2026-06-15T09:30:44Z

Updating 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 the latest evaluations.

…inement_stage_max_edges_to_remove default values

github-actions · 2026-06-15T09:32:18Z

`nf-core pipelines lint` overall result: Passed ✅

Posted for pipeline commit 7225268

+| ✅ 231 tests passed       |+
#| ❔   9 tests were ignored |#

Details

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: tests/default.nf.test
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-pixelator_logo_light.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
multiqc_config - multiqc_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-pixelator_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/CONTRIBUTING.md
files_exist - File found: docs/images/nf-core-pixelator_logo_light.png
files_exist - File found: docs/images/nf-core-pixelator_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: main.nf
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-pixelator_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowPixelator.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 4.2.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.pna_amplicon_mismatches= 0.1
nextflow_config - Config default value correct: params.pna_amplicon_remove_polyg= true
nextflow_config - Config default value correct: params.pna_amplicon_quality_cutoff= 20
nextflow_config - Config default value correct: params.pna_amplicon_low_complexity_filter= true
nextflow_config - Config default value correct: params.pna_amplicon_low_complexity_threshold= 0.8
nextflow_config - Config default value correct: params.pna_amplicon_lbs_filter= true
nextflow_config - Config default value correct: params.pna_amplicon_lbs_filter_min_overlap= 8
nextflow_config - Config default value correct: params.pna_amplicon_lbs_filter_error_rate= 0.1
nextflow_config - Config default value correct: params.pna_demux_mismatches= 1
nextflow_config - Config default value correct: params.pna_demux_output_chunk_reads= 50M
nextflow_config - Config default value correct: params.pna_demux_output_max_chunks= 8
nextflow_config - Config default value correct: params.pna_demux_strategy= independent
nextflow_config - Config default value correct: params.pna_collapse_algorithm= directional
nextflow_config - Config default value correct: params.pna_collapse_mismatches= 2
nextflow_config - Config default value correct: params.pna_graph_multiplet_recovery= true
nextflow_config - Config default value correct: params.pna_graph_initial_stage_leiden_resolution= 1.0
nextflow_config - Config default value correct: params.pna_graph_refinement_stage_leiden_resolution= 0.5
nextflow_config - Config default value correct: params.pna_graph_edge_cycle_verification= true
nextflow_config - Config default value correct: params.pna_graph_min_count= 1.0
nextflow_config - Config default value correct: params.pna_graph_max_refinement_recursion_depth= 3
nextflow_config - Config default value correct: params.pna_graph_initial_stage_max_edges_to_remove= 10
nextflow_config - Config default value correct: params.pna_graph_refinement_stage_max_edges_to_remove= 20
nextflow_config - Config default value correct: params.pna_graph_component_size_min_threshold= 8000
nextflow_config - Config default value correct: params.pna_sample_calling_remove_incompatible= true
nextflow_config - Config default value correct: params.pna_sample_calling_enrichment_threshold= 10.0
nextflow_config - Config default value correct: params.pna_denoise_pval_threshold= 0.05
nextflow_config - Config default value correct: params.pna_denoise_inflate_factor= 1.5
nextflow_config - Config default value correct: params.pna_denoise_run_ace_denoising= true
nextflow_config - Config default value correct: params.pna_denoise_ace_k= 3
nextflow_config - Config default value correct: params.pna_denoise_run_pls_denoising= true
nextflow_config - Config default value correct: params.pna_denoise_pls_score_threshold= -3.0
nextflow_config - Config default value correct: params.pna_analysis_compute_proximity= true
nextflow_config - Config default value correct: params.pna_analysis_compute_k_cores= true
nextflow_config - Config default value correct: params.pna_analysis_proximity_nbr_of_permutations= 100
nextflow_config - Config default value correct: params.pna_analysis_compute_svd_var_explained= true
nextflow_config - Config default value correct: params.pna_analysis_svd_nbr_of_pivots= 50
nextflow_config - Config default value correct: params.pna_layout_layout_algorithm= coarsened_pmds_3d
nextflow_config - Config default value correct: params.pna_layout_pmds_pivots= 50
nextflow_config - Config default value correct: params.pna_layout_wpmds_k= 5
nextflow_config - Config default value correct: params.save_json= true
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/e8950f260973a6778e2ff24988e12fd4474d60e1/
nextflow_config - Config default value correct: params.modules_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/
nf_test_content - 'tests/proxiome_v1.nf.test' contains outdir parameter
nf_test_content - 'tests/proxiome_v1.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v1.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v1.nf.test' contains outdir parameter
nf_test_content - 'tests/proxiome_v1.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v2.nf.test' contains outdir parameter
nf_test_content - 'tests/proxiome_v2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v2.nf.test' contains outdir parameter
nf_test_content - 'tests/proxiome_v2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/images/nf-core-pixelator_logo_light.png matches the template
files_unchanged - docs/images/nf-core-pixelator_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 25.10.4, Config: 25.10.4
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - PIXELATOR found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_LIST_OPTIONS found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 4.0.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 4.0.2
Run at 2026-06-22 14:02:34

ptajvar · 2026-06-15T09:55:15Z

Some of the tests are failing with the parameter changes. Will look into it.

…t-default-parameters

ptajvar added 2 commits June 15, 2026 09:27

update pna_graph_refinement_stage_leiden_resolution and pna_graph_ref…

29edc94

…inement_stage_max_edges_to_remove default values

update CHANGELOG.md

dbadda3

ptajvar requested a review from a team as a code owner June 15, 2026 09:30

ptajvar requested a review from Aratz June 15, 2026 09:31

ptajvar marked this pull request as draft June 15, 2026 09:54

ptajvar and others added 7 commits June 15, 2026 11:06

lower pna_graph_component_size_min_threshold for v2 test

234b741

lower pna_graph_component_size_min_threshold for v2 test to 2

873851e

set pna_graph_component_size_min_threshold to 10 for both v1 and v2

cdaec15

set test pna_graph_component_size_min_threshold to 25

3ec7e58

Update pixelatorES to 0.11.2

43edcd2

Merge remote-tracking branch 'origin/dev' into update-graph-refinemen…

93de027

…t-default-parameters

Roll back graph parameters for test profile

7225268

Aratz marked this pull request as ready for review June 22, 2026 14:05

Aratz approved these changes Jun 22, 2026

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Aratz merged commit a2470e2 into dev Jun 22, 2026
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update pna_graph_refinement_stage_leiden_resolution and pna_graph_ref…#226

update pna_graph_refinement_stage_leiden_resolution and pna_graph_ref…#226
Aratz merged 9 commits into
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update-graph-refinement-default-parameters

ptajvar commented Jun 15, 2026

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github-actions Bot commented Jun 15, 2026 •

edited

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❔ Tests ignored:

✅ Tests passed:

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ptajvar commented Jun 15, 2026

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ptajvar commented Jun 15, 2026

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nf-core pipelines lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

ptajvar commented Jun 15, 2026

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github-actions Bot commented Jun 15, 2026 •

edited

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`nf-core pipelines lint` overall result: Passed ✅