Make testing suite work on any hardware by nictru · Pull Request #274 · nf-core/scdownstream

nictru · 2026-03-24T15:42:07Z

No description provided.

github-actions · 2026-03-24T15:44:03Z

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

Posted for pipeline commit ded90e2

+| ✅ 275 tests passed       |+
#| ❔   1 tests had warnings |#
!| ❗  14 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ 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/CONTRIBUTING.md
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-scdownstream_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/images/nf-core-scdownstream_logo_light.png
files_exist - File found: docs/images/nf-core-scdownstream_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: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
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-scdownstream_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/WorkflowScdownstream.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: 0.0.1dev
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.duplicate_var_resolution= sum
nextflow_config - Config default value correct: params.species= human
nextflow_config - Config default value correct: params.cell_cycle_scoring= true
nextflow_config - Config default value correct: params.ambient_correction= decontx
nextflow_config - Config default value correct: params.ambient_corrected_integration= false
nextflow_config - Config default value correct: params.doublet_detection= scrublet
nextflow_config - Config default value correct: params.doublet_detection_threshold= 1
nextflow_config - Config default value correct: params.cellbender_epochs= 150
nextflow_config - Config default value correct: params.integration_methods= scvi
nextflow_config - Config default value correct: params.integration_hvgs= 0
nextflow_config - Config default value correct: params.scimilarity_model= https://zenodo.org/records/10685499/files/model_v1.1.tar.gz
nextflow_config - Config default value correct: params.base_label_col= label
nextflow_config - Config default value correct: params.base_condition_col= condition
nextflow_config - Config default value correct: params.clustering_resolutions= 0.5,1.0
nextflow_config - Config default value correct: params.cluster_global= true
nextflow_config - Config default value correct: params.memory_scale= 1
nextflow_config - Config default value correct: params.rankgenesgroups_method= wilcoxon
nextflow_config - Config default value correct: params.scvi_n_latent= 30
nextflow_config - Config default value correct: params.scvi_n_hidden= 128
nextflow_config - Config default value correct: params.scvi_n_layers= 2
nextflow_config - Config default value correct: params.scvi_dispersion= gene
nextflow_config - Config default value correct: params.scvi_gene_likelihood= zinb
nextflow_config - Config default value correct: params.pseudobulk_groupby_labels= batch
nextflow_config - Config default value correct: params.pseudobulk_min_num_cells= 5
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.max_multiqc_email_size= 25.MB
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/3ba0ba7174a5667fc2e005430594ffb063f986c7/
nf_test_content - 'tests/main_pipeline_build.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_build.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_build.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_reference_mapping.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_reference_mapping.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_reference_mapping.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_extend.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_extend.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_extend.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_qc.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_qc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_qc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_sub.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_sub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_sub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_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 - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md 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/PULL_REQUEST_TEMPLATE.md 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 - assets/nf-core-scdownstream_logo_light.png matches the template
files_unchanged - docs/images/nf-core-scdownstream_logo_light.png matches the template
files_unchanged - docs/images/nf-core-scdownstream_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore 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: 25.10.0, Config: 25.10.0
readme - README nf-core template version badge 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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
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 - GET_ found in conf/modules.config and Nextflow scripts.
modules_config - COLLECT_SIZES found in conf/modules.config and Nextflow scripts.
modules_config - QC_RAW found in conf/modules.config and Nextflow scripts.
modules_config - QC_FILTERED found in conf/modules.config and Nextflow scripts.
modules_config - CELDA_DECONTX found in conf/modules.config and Nextflow scripts.
modules_config - SOUPX found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - SCVITOOLS_SOLO found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_SCRUBLET found in conf/modules.config and Nextflow scripts.
modules_config - DOUBLETDETECTION found in conf/modules.config and Nextflow scripts.
modules_config - SCDS found in conf/modules.config and Nextflow scripts.
modules_config - DOUBLET_REMOVAL found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_CELLCYCLE found in conf/modules.config and Nextflow scripts.
modules_config - FINALIZE_QC_ANNDATAS found in conf/modules.config and Nextflow scripts.
modules_config - MYGENE found in conf/modules.config and Nextflow scripts.
modules_config - SET_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - HUGOUNIFIER_GET found in conf/modules.config and Nextflow scripts.
modules_config - HUGOUNIFIER_APPLY found in conf/modules.config and Nextflow scripts.
modules_config - ADATA_UNIFY found in conf/modules.config and Nextflow scripts.
modules_config - ADATA_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - ADATA_UPSETGENES found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_HVGS found in conf/modules.config and Nextflow scripts.
modules_config - SCVITOOLS_SCVI found in conf/modules.config and Nextflow scripts.
modules_config - SCVITOOLS_SCANVI found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_HARMONY found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_BBKNN found in conf/modules.config and Nextflow scripts.
modules_config - SEURAT_INTEGRATION found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_COMBAT found in conf/modules.config and Nextflow scripts.
modules_config - SCIMILARITY_EMBED found in conf/modules.config and Nextflow scripts.
modules_config - SCIMILARITY_ANNOTATE found in conf/modules.config and Nextflow scripts.
modules_config - ADATA_MERGEEMBEDDINGS found in conf/modules.config and Nextflow scripts.
modules_config - CELLDEX_FETCHREFERENCE found in conf/modules.config and Nextflow scripts.
modules_config - CELLTYPES_SINGLER found in conf/modules.config and Nextflow scripts.
modules_config - CELLTYPES_CELLTYPIST found in conf/modules.config and Nextflow scripts.
modules_config - NEIGHBORS found in conf/modules.config and Nextflow scripts.
modules_config - LEIDEN found in conf/modules.config and Nextflow scripts.
modules_config - ENTROPY found in conf/modules.config and Nextflow scripts.
modules_config - UMAP found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_PAGA found in conf/modules.config and Nextflow scripts.
modules_config - LIANA_RANKAGGREGATE found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_RANKGENESGROUPS found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC 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: 3.5.2
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-03-25 15:22:22

Disable OpenMP CPU topology detection for MacOS compatibility

nictru added 2 commits March 24, 2026 14:35

Make several tests structure-based instead of hash-based

531e90e

Remove doubletdetection from pipeline-level tests

8c4135c

nictru and others added 11 commits March 24, 2026 19:36

Update test snapshots

79ac2d1

Update CI nf-test version

3ba8985

Disable OpenMP CPU topology detection

d0c5e97

Disable OpenMP CPU topology detection for MacOS compatibility

Add MPLCONFIGDIR to PREPCELLXGENE module

e93537c

Add missing CPU topology detection disables

2d40395

Update snapshots

278b7e6

Simplify umap tests

32210e4

Update HVG tests

25eab93

Update SCDS tests

ec3648d

Simplify per-group tests

6af93ad

Update testing strategy

ded90e2

Provide feedback

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Make testing suite work on any hardware#274

Make testing suite work on any hardware#274
nictru wants to merge 13 commits intodevfrom
lenient-testing

nictru commented Mar 24, 2026

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github-actions bot commented Mar 24, 2026 •

edited

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✅ Tests passed:

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nictru commented Mar 24, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests fixed:

✅ Tests passed:

Run details

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github-actions bot commented Mar 24, 2026 •

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