Migrate to channel topics by fasterius · Pull Request #133 · nf-core/spatialvi

fasterius · 2026-01-27T14:39:10Z

This PR adds usage of channel topics for the pipeline. Currently waiting for nf-core/modules#9787 (SPACERANGER_COUNT) and nf-core/modules#9749 (UNTAR) module PRs to be merged before this PR can be finished.

PR checklist

This comment contains a description of changes (with reason).
Make sure your code lints (nf-core pipelines lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
CHANGELOG.md is updated.

github-actions · 2026-01-27T14:40:45Z

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

Posted for pipeline commit 4c09a31

+| ✅ 214 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   6 tests had warnings |!

Details

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_unchanged - File ignored due to lint config: .gitattributes
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-spatialvi_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialvi_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialvi_logo_dark.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ 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-spatialvi_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-spatialvi_logo_light.png
files_exist - File found: docs/images/nf-core-spatialvi_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-spatialvi_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/WorkflowSpatialvi.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: 1.0dev
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.spaceranger_reference= https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-GRCh38-2020-A.tar.gz
nextflow_config - Config default value correct: params.hd_bin_size= 8
nextflow_config - Config default value correct: params.qc_min_counts= 500
nextflow_config - Config default value correct: params.qc_min_genes= 250
nextflow_config - Config default value correct: params.qc_min_spots= 1
nextflow_config - Config default value correct: params.qc_mito_threshold= 20.0
nextflow_config - Config default value correct: params.qc_ribo_threshold= 0.0
nextflow_config - Config default value correct: params.qc_hb_threshold= 100.0
nextflow_config - Config default value correct: params.cluster_n_hvgs= 2000
nextflow_config - Config default value correct: params.cluster_resolution= 1.0
nextflow_config - Config default value correct: params.svg_autocorr_method= moran
nextflow_config - Config default value correct: params.n_top_svgs= 14
nextflow_config - Config default value correct: params.integration_cluster_resolution= 1.0
nextflow_config - Config default value correct: params.integration_n_hvgs= 2000
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/
nf_test_content - 'tests/test_downstream.nf.test' contains outdir parameter
nf_test_content - 'tests/test_downstream.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/test_spaceranger_ffpe_hd.nf.test' contains outdir parameter
nf_test_content - 'tests/test_spaceranger_ffpe_hd.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_spaceranger_ffpe_v1.nf.test' contains outdir parameter
nf_test_content - 'tests/test_spaceranger_ffpe_v1.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 - .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/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/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: 25.04.0, Config: 25.04.0
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: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting_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: nf-test.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.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 - SPACERANGER_UNTAR_REFERENCE found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR_SPACERANGER_INPUT found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - SPACERANGER_COUNT found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - READ_DATA found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_SDATA found in conf/modules.config and Nextflow scripts.
modules_config - INTEGRATE_SDATA 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: 3.5.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.1
Run at 2026-02-12 09:02:15

fasterius · 2026-01-29T13:22:49Z

UNTAR is included in another PR: nf-core/modules#9796.

nf-core-bot · 2026-02-06T11:50:16Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

fasterius · 2026-02-06T16:40:36Z

@cavenel Did something change in the Visium HD tests? It's running out of time, and the latest commits I see for the test_spaceranger_hd_ffpe were 5 months ago.

cavenel · 2026-02-11T09:24:30Z

Except from the version of SpaceRanger I don't think anything changed... Maybe the running time is around 1h and sometimes take longer? I guess we could just increase to 2h for this test.

3 weeks ago the whole test 3/4 took 38 minutes, so quite far from 1h. I tried to run it again, we will see.

fasterius added 11 commits January 23, 2026 07:45

Update MultiQC module

26281ee

Update FastQC module

25e46a4

Update QUARTONOTEBOOK module

b102087

Update Space Ranger count module

93e79b1

Update subworkflows

1b310bd

Merge branch 'dev' into topics

1d14f99

Fix formatting for strict mode

07c3238

Update QUARTONOTEBOOK module (topics)

9fe4c69

Fix local copy of spaceranger/count

a32be94

Use topics for READ_DATA local module

82f428a

Use topics for MERGE_SDATA local module

20c9827

fasterius changed the title ~~Topics~~ Migrate to channel topics Jan 27, 2026

Update SPACERANGER_COUNT with topics

bb27766

fasterius added 5 commits February 6, 2026 12:22

Merge branch 'dev' into topics

7d83d3f

Update UNTAR nf-core module with topics

a955cec

Update FASTQC nf-core module

166d7fd

Update MULTIQC nf-core module

0fc823c

Remove remaining redundant ch_versions usage

bdf6249

Update snapshots

74f9851

Update CHANGELOG

5d4276f

fasterius added 2 commits February 11, 2026 11:21

Try increasing time limit for HD test to 2h

bd5e3a1

Use test_spaceranger_hd profile in nf-test HD

34e2544

fasterius marked this pull request as ready for review February 11, 2026 14:05

Update HD snapshots

4c09a31

cavenel approved these changes Feb 12, 2026

View reviewed changes

fasterius merged commit a4bd0e6 into dev Feb 12, 2026
15 checks passed

fasterius deleted the topics branch February 12, 2026 13:06

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Migrate to channel topics#133

Migrate to channel topics#133
fasterius merged 22 commits intodevfrom
topics

fasterius commented Jan 27, 2026 •

edited

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github-actions bot commented Jan 27, 2026 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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fasterius commented Jan 29, 2026

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nf-core-bot commented Feb 6, 2026

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fasterius commented Feb 6, 2026 •

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cavenel commented Feb 11, 2026 •

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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fasterius commented Jan 29, 2026

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fasterius commented Jan 27, 2026 •

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github-actions bot commented Jan 27, 2026 •

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

fasterius commented Feb 6, 2026 •

edited

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cavenel commented Feb 11, 2026 •

edited

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