Release 1.2.0 - Cartography Castle by FloWuenne · Pull Request #128 · nf-core/molkart

FloWuenne · 2025-10-27T07:44:36Z

Description

This PR will update the master branch for the next release 1.2.0 Cartography Castle.

Bump versions after release 1.1.0.

Add cellpose parameter cellprob_threshold to the pipeline. Issue #92

solved training images issue

Json schema improvements

Local stubs

Use nf-test in CI

Template conflicts

Merging template updates 3.4.1

github-actions · 2025-10-27T07:47:35Z

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

Posted for pipeline commit b30ee0e

+| ✅ 253 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

Details

❗ Test warnings:

pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: conf/igenomes.config
files_unchanged - File ignored due to lint config: assets/nf-core-molkart_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-molkart_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-molkart_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-molkart_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-molkart_logo_light.png
files_exist - File found: docs/images/nf-core-molkart_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-molkart_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/WorkflowMolkart.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 does not contain dev for release: 1.2.0
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.segmentation_method= mesmer
nextflow_config - Config default value correct: params.cellpose_diameter= 30
nextflow_config - Config default value correct: params.cellpose_chan= 0
nextflow_config - Config default value correct: params.cellpose_pretrained_model= cyto
nextflow_config - Config default value correct: params.cellpose_flow_threshold= 0.4
nextflow_config - Config default value correct: params.cellpose_edge_exclude= true
nextflow_config - Config default value correct: params.cellpose_cellprob_threshold= 0
nextflow_config - Config default value correct: params.mesmer_image_mpp= 0.138
nextflow_config - Config default value correct: params.mesmer_compartment= whole-cell
nextflow_config - Config default value correct: params.stardist_model= 2D_versatile_fluo
nextflow_config - Config default value correct: params.stardist_n_tiles_x= 3
nextflow_config - Config default value correct: params.stardist_n_tiles_y= 3
nextflow_config - Config default value correct: params.mindagap_boxsize= 3
nextflow_config - Config default value correct: params.mindagap_loopnum= 40
nextflow_config - Config default value correct: params.clahe_cliplimit= 0.01
nextflow_config - Config default value correct: params.clahe_nbins= 256
nextflow_config - Config default value correct: params.clahe_pixel_size= 0.138
nextflow_config - Config default value correct: params.clahe_kernel= 25.0
nextflow_config - Config default value correct: params.mindagap_tilesize= 2144
nextflow_config - Config default value correct: params.clahe_pyramid_tile= 1072
nextflow_config - Config default value correct: params.crop_size_x= 400
nextflow_config - Config default value correct: params.crop_size_y= 400
nextflow_config - Config default value correct: params.crop_amount= 4
nextflow_config - Config default value correct: params.crop_nonzero_fraction= 0.4
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/
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/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/main.nf.test' contains outdir parameter
nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main.nf.test' contains outdir parameter
nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main.nf.test' contains outdir parameter
nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main.nf.test' contains outdir parameter
nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main.nf.test' contains outdir parameter
nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main.nf.test' contains outdir parameter
nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main.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 - 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.
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: 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.
base_config - ILASTIK_PIXELCLASSIFICATION found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - MOLKARTQC found in conf/modules.config and Nextflow scripts.
modules_config - MOLKARTQCPNG found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_STACK found in conf/modules.config and Nextflow scripts.
modules_config - MASKFILTER found in conf/modules.config and Nextflow scripts.
modules_config - MINDAGAP_MINDAGAP found in conf/modules.config and Nextflow scripts.
modules_config - MINDAGAP_DUPLICATEFINDER found in conf/modules.config and Nextflow scripts.
modules_config - SPOT2CELL found in conf/modules.config and Nextflow scripts.
modules_config - ILASTIK_PIXELCLASSIFICATION found in conf/modules.config and Nextflow scripts.
modules_config - ILASTIK_MULTICUT found in conf/modules.config and Nextflow scripts.
modules_config - CROPHDF5 found in conf/modules.config and Nextflow scripts.
modules_config - CROPTIFF found in conf/modules.config and Nextflow scripts.
modules_config - TIFFH5CONVERT found in conf/modules.config and Nextflow scripts.
modules_config - CLAHE found in conf/modules.config and Nextflow scripts.
modules_config - STARDIST found in conf/modules.config and Nextflow scripts.
modules_config - DEEPCELL_MESMER found in conf/modules.config and Nextflow scripts.
modules_config - CELLPOSE found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_ANNDATA 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: 3.4.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 1.2.0, nfcore_yml.version = 1.2.0

Run details

nf-core/tools version 3.4.1
Run at 2025-10-27 07:47:11

FloWuenne and others added 30 commits March 6, 2025 16:59

Version bump on dev after release 1.1.0.

458b4be

[automated] Fix code linting

0b69562

Merge pull request #108 from nf-core/postrelease_1.1.0

4b7467d

Bump versions after release 1.1.0.

Add cellpose cellprob_threshold parameter #92

3d11386

Build nextflow_schema

3b6b1cd

Merge pull request #109 from felixS27/master

b77ca7f

Add cellpose parameter cellprob_threshold to the pipeline. Issue #92

solved issue

cbd0fa5

updated test

97b74e2

Merge pull request #110 from miri-2000/training_images_issue

068b409

solved training images issue

updated schemas

535199e

Merge pull request #113 from kbestak/json-schema-improvements

17cd243

Json schema improvements

added local stubs and tests

d56cb06

updated mesmer module

8f01792

updated changelog

1afc815

Merge pull request #115 from kbestak/local-stubs

9a3b10f

Local stubs

adapted ci

7c55e78

modified changelog

bde9b09

env fix

1718623

fix ci

c71cc6a

ci resource management

e2ca6a4

updated multiqc

815023a

updated .nftignore

992a206

mindagap - markedDups.txt tmp in .nftignore

7395d5f

updated mindagap

b1d674b

updated mindagap

381fd15

Template update for nf-core/tools version 3.2.1

946f853

Merge pull request #116 from kbestak/test_updates

6ee8674

Use nf-test in CI

resolved template update conflicts

4496a7a

updated CHANGELOG

211d4fe

Template update for nf-core/tools version 3.3.1

810a29d

kbestak and others added 25 commits October 21, 2025 15:36

merging template updates

211f0e9

updated multiqc

0fc8afc

updated ro-crate-metadata

e0faf55

fix files unchanged

0ea33a6

updated test config

88371c5

updated changelog

57c6f13

fix pre-commit formatting (trailing whitespace)

41f8f4c

changelog and devcontainer

7349f28

fixed files unchanged

731a5ee

fix trailing whitespace

7368d15

copied pull request template even though local linting passed

6c388b7

disk large because tests were running out of space

b3f8580

Merge pull request #124 from kbestak/template-conflicts

ca17fac

Template conflicts

Update pipeline level snapshots.

7277fe0

Fix disk label for nf-test runner.

f658318

Change syntax for runner size.

c644ab1

Add default nf-test snapshot.

cc9d38b

Apply right nf-test version, exclude unstable output.

9b96e76

Merge pull request #125 from nf-core/merging-template-updates-3.4.1

5498530

Merging template updates 3.4.1

Bump version for release.

65889a6

Fixing lint errors.

97ede71

Update snapshot release version.

99f5f00

Update PULL_REQUEST_TEMPLATE.md to be in line with template.

a0a8b3b

Update default nf-test snapshot for version,

b936cfc

Merge pull request #127 from FloWuenne/bump_release_1.2.0

b30ee0e

robsyme self-requested a review October 27, 2025 08:29

edmundmiller approved these changes Oct 27, 2025

View reviewed changes

robsyme approved these changes Oct 27, 2025

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FloWuenne merged commit 4ec0790 into master Oct 27, 2025
68 of 70 checks passed

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Release 1.2.0 - Cartography Castle#128

Release 1.2.0 - Cartography Castle#128
FloWuenne merged 58 commits intomasterfrom
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FloWuenne commented Oct 27, 2025 •

edited

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github-actions Bot commented Oct 27, 2025 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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FloWuenne commented Oct 27, 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:

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FloWuenne commented Oct 27, 2025 •

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github-actions Bot commented Oct 27, 2025 •

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