Support lower image resolution by quentinblampey · Pull Request #30 · nf-core/sopa

quentinblampey · 2026-07-23T11:45:13Z

Recently, we added in sopa the possibility to run cell segmentation on lower resolution images. This can be useful when we want to compute a segmentation quickly and use it as a prior for later re-segmentation, e.g., with proseg.

This PR adds support fort this feature in nf-core/sopa.

and also prepare for the v1.0.1 release

nf-core-bot · 2026-07-23T11:49:18Z

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.

github-actions · 2026-07-23T11:50:22Z

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

Posted for pipeline commit ba848f5

+| ✅ 205 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.0.1
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
local_component_structure - utils.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
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: assets/multiqc_config.yml
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: assets/nf-core-sopa_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sopa_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sopa_logo_dark.png
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/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-sopa_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-sopa_logo_light.png
files_exist - File found: docs/images/nf-core-sopa_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: 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-sopa_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/WorkflowSopa.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 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.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/
nextflow_config - Config default value correct: params.technology= xenium
nextflow_config - Config default value correct: params.min_area_pixels2= 0.0
nextflow_config - Config default value correct: params.min_area_microns2= 0.0
nextflow_config - Config default value correct: params.pixel_size= 0.2125
nextflow_config - Config default value correct: params.lazy= true
nextflow_config - Config default value correct: params.ram_threshold_gb= 4.0
nextflow_config - Config default value correct: params.mean_cell_diameter= 10.0
nextflow_config - Config default value correct: params.max_cell_radius= 15.0
nextflow_config - Config default value correct: params.alpha= 0.5
nextflow_config - Config default value correct: params.min_rna_per_cell= 1.0
nextflow_config - Config default value correct: params.baysor_scale= -1.0
nextflow_config - Config default value correct: params.baysor_scale_std= 25%
nextflow_config - Config default value correct: params.prior_segmentation_confidence= 0.2
nextflow_config - Config default value correct: params.min_molecules_per_cell= 20.0
nextflow_config - Config default value correct: params.min_molecules_per_gene= 10.0
nextflow_config - Config default value correct: params.force_2d= true
nf_test_content - 'tests/cellpose.nf.test' contains outdir parameter
nf_test_content - 'tests/cellpose.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/cellpose.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/baysor.nf.test' contains outdir parameter
nf_test_content - 'tests/baysor.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/baysor.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/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 - 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: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
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: clean-up.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: linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting_comment.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.
base_config - PATCH_SEGMENTATION_PROSEG found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - SPACERANGER_COUNT 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 2026-07-23 11:56:01

alihamraoui

Awsome @quentinblampey. Thanks

support scale > 0

19fe4a5

quentinblampey changed the base branch from master to dev July 23, 2026 11:45

nf-core deleted a comment from github-actions Bot Jul 23, 2026

quentinblampey requested a review from alihamraoui July 23, 2026 11:46

bump version for future 1.0.1 release

be6771c

nf-core deleted a comment from github-actions Bot Jul 23, 2026

update snapshots

ba848f5

alihamraoui approved these changes Jul 23, 2026

View reviewed changes

quentinblampey merged commit dcd263b into dev Jul 23, 2026
13 checks passed

quentinblampey deleted the support_lower_scales branch July 23, 2026 12:12

quentinblampey mentioned this pull request Jul 23, 2026

Merge dev into master to release the version 1.0.1 #31

Merged

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Support lower image resolution - #30

Support lower image resolution#30
quentinblampey merged 3 commits into
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support_lower_scales

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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✅ Tests passed:

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quentinblampey commented Jul 23, 2026 •

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