Segmentation report by mcmero · Pull Request #7 · WEHI-SODA-Hub/sp_segment

mcmero · 2025-09-12T00:39:20Z

Add segmentation report.

PR checklist

github-actions · 2025-09-12T00:39:28Z

This PR is against the `main` branch ❌

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It looks like this pull-request is has been made against the WEHI-SODA-Hub/spatialproteomics main branch.
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Because of this, PRs to main are only allowed if they come from the WEHI-SODA-Hub/spatialproteomics dev branch.

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Thanks again for your contribution!

github-actions · 2025-09-12T00:40:41Z

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

Posted for pipeline commit 434f0a7

+| ✅  87 tests passed       |+
#| ❔  25 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 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 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!

❔ 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: conf/test.config
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/nf-test.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/workflows/fix-linting.yml
files_exist - File is ignored: .github/actions/get-shards/action.yml
files_exist - File is ignored: .github/actions/nf-test/action.yml
files_exist - File is ignored: .github/actions/
files_exist - File is ignored: assets/nf-core-spatialproteomics_logo_light.png
files_exist - File is ignored: docs/images/nf-core-spatialproteomics_logo_light.png
files_exist - File is ignored: docs/images/nf-core-spatialproteomics_logo_dark.png
files_exist - File is ignored: tests/default.nf.test
nextflow_config - nextflow_config
files_unchanged - Required pipeline config not found - {'manifest.contributors'}
actions_nf_test - '.github/workflows/nf-test.yml' not found
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/spatialproteomics/spatialproteomics/.github/workflows/awstest.yml
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/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/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: conf/modules.config
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: 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-spatialproteomics_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/WorkflowSpatialproteomics.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
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
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
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_comment.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: ci.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.
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: 3.3.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.3.2
Run at 2025-09-12 00:46:07

mcmero added 11 commits September 1, 2025 13:54

Add segmentation report module

547bb18

Implement report generation into mesmer and sopa subworkflows

70ece04

Update to use latest report generation with mesmer/cellpose params

b2b2701

Update spatialvis version with report improvements

94750a9

Update workflow diagram and add mermaid source

7327959

Update spatialvis version

9d2aea0

Sync ro-crate file

ea5e810

Lint fixes

4857e66

Update README

2f95ac3

Update tests

ef5895d

Update change log

346c794

mcmero changed the title ~~Segmentationreport~~ Segmentation report Sep 12, 2025

mcmero changed the base branch from main to dev September 12, 2025 00:40

Update version

434f0a7

mcmero merged commit 1b1b11a into dev Sep 12, 2025
5 checks passed

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Segmentation report - #7

Segmentation report#7
mcmero merged 12 commits into
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segmentationreport

mcmero commented Sep 12, 2025

Uh oh!

github-actions Bot commented Sep 12, 2025

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github-actions Bot commented Sep 12, 2025 •

edited

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mcmero commented Sep 12, 2025

PR checklist

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github-actions Bot commented Sep 12, 2025

This PR is against the main branch ❌

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github-actions Bot commented Sep 12, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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This PR is against the `main` branch ❌

github-actions Bot commented Sep 12, 2025 •

edited

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