Updated pipeline to run on the latest versions of Nextflow by cgoina · Pull Request #2 · JaneliaSciComp/nf-cellpose

cgoina · 2026-07-01T14:42:44Z

Updated the pipeline to make it compliant with newer version of Nextflow
Added parameters to support sharded ZARR v3 output
Support for Cellpose 4.2.1 and newer models: cpsam_v2, cpdino, cpdino-vitb, and cpsam
The pipeline now requires Nextflow 25.10.0 because of updated nf-schema plugin

github-actions · 2026-07-02T03:45:07Z

`nf-core pipelines lint` overall result: Failed ❌

Posted for pipeline commit 63d90e1

+| ✅ 189 tests passed       |+
#| ❔  23 tests were ignored |#
!| ❗  19 tests had warnings |!
-| ❌   3 tests failed       |-

Details

❌ Test failures:

version_consistency - nfcore_yml.version was not numeric: 1.0.0dev!
version_consistency - The versioning is not consistent between container, release tag and config. Found manifest.version = 1.1.0, nfcore_yml.version = 1.0.0dev
included_configs - Pipeline config does not include custom configs. Please uncomment the includeConfig line.

❗ Test warnings:

files_exist - File not found: assets/multiqc_config.yml
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 nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
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
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
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_if_empty_null - ifEmpty(null) found in /home/runner/work/nf-cellpose/nf-cellpose/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
_
pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters
schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-nf-cellpose_logo_light.png
files_exist - File is ignored: docs/images/nf-core-nf-cellpose_logo_light.png
files_exist - File is ignored: docs/images/nf-core-nf-cellpose_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nextflow_config - Config default ignored: params.zarr_compression_opts
nextflow_config - Config default ignored: params.dask_config
files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/nf-core-nf-cellpose_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-nf-cellpose_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-nf-cellpose_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/nf-cellpose/nf-cellpose/.github/workflows/awstest.yml
modules_json - modules_json
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: 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/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/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: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/CONTRIBUTING.md
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: 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-nf-cellpose_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/WorkflowNf-cellpose.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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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 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: 1.1.0
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.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.cellpose_model= cpsam
nextflow_config - Config default value correct: params.anisotropy= 0.0
nextflow_config - Config default value correct: params.expansion_factor= 1.0
nextflow_config - Config default value correct: params.timeindex= 0.0
nextflow_config - Config default value correct: params.cellpose_cpus= 1
nextflow_config - Config default value correct: params.cellpose_mem_gb= 0
nextflow_config - Config default value correct: params.process_blocksize= 256,256,256
nextflow_config - Config default value correct: params.local_workers= 1
nextflow_config - Config default value correct: params.do_3D= true
nextflow_config - Config default value correct: params.use_gpu= true
nextflow_config - Config default value correct: params.skip_normalize= false
nextflow_config - Config default value correct: params.norm_percentile= 1 99
nextflow_config - Config default value correct: params.stitch_threshold= 0.0
nextflow_config - Config default value correct: params.cellprob_threshold= 1.0
nextflow_config - Config default value correct: params.flow3D_smooth= 1
nextflow_config - Config default value correct: params.niter= 0
nextflow_config - Config default value correct: params.min_size= 15
nextflow_config - Config default value correct: params.merge_labels_distance_th= 1
nextflow_config - Config default value correct: params.zarr_format= 3
nextflow_config - Config default value correct: params.zarr_chunksize= 64,64,64
nextflow_config - Config default value correct: params.zarr_sharding_factor= 4,4,4
nextflow_config - Config default value correct: params.zarr_compression= zstd
nextflow_config - Config default value correct: params.mergelabels_distance_th= 1
nextflow_config - Config default value correct: params.mergelabels_cpus= 1
nextflow_config - Config default value correct: params.mergelabels_mem_gb= 0
nextflow_config - Config default value correct: params.multiscale_cpus= 1
nextflow_config - Config default value correct: params.multiscale_mem_gb= 0
nextflow_config - Config default value correct: params.dask_workers= 1
nextflow_config - Config default value correct: params.dask_min_workers= 1
nextflow_config - Config default value correct: params.dask_scheduler_port= 0
nextflow_config - Config default value correct: params.dask_dashboard_port= 0
nextflow_config - Config default value correct: params.dask_worker_cpus= 1
nextflow_config - Config default value correct: params.dask_worker_mem_gb= 0
nextflow_config - Config default value correct: params.dask_start_timeout_secs= 300
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.default_mem_gb_per_cpu= 15
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 - LICENSE matches the template
files_unchanged - .github/.dockstore.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/sendmail_template.txt 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
readme - README Nextflow minimum version badge matched config. Badge: 25.10.0, Config: 25.10.0
readme - README nf-core template version badge found.
plugin_includes - No wrong validation plugin imports have been found
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
merge_markers - No merge markers found in pipeline files
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: 4.0.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 4.0.2
Run at 2026-07-02 03:44:37

cgoina added 24 commits January 27, 2026 11:35

update dask

10ded70

a first pass of updating the code to be v2 parser compliant

974e099

replaced local multiscale subworkflow with the one from nextflow-modules

5dba8eb

update cellpose tools:

374639e

update multiscale module

a01ae47

removed dumpHashes arg

848f80e

cellpose niter arg

b8661cc

allow gpu device to be int

86876c7

cast parameters

8f3aae7

set lenient mode

d480018

upate modules - removed cpus and memory from module input params

5c13155

cast dask workers to int

83a58ff

upgrade cellpose

5c5d786

use cellpose container for multiscale too

ae031a3

set errorstrategy for omezarr tools

9380933

updated cellpose container runtime and cluster option arguments

cad1c51

update cellpose-tools

e38a822

update conda env for segtools modules

1218608

update cellpose tools

1a7fe38

updated changelog

88f6d63

update changelog

26ce6a2

auto fixed by linter

eba580f

lint fixes

22c47e5

update subworkflows

63d90e1

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Uh oh!

Updated pipeline to run on the latest versions of Nextflow#2

Updated pipeline to run on the latest versions of Nextflow#2
cgoina wants to merge 24 commits into
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cgoina commented Jul 1, 2026

Uh oh!

github-actions Bot commented Jul 2, 2026

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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cgoina commented Jul 1, 2026

Uh oh!

github-actions Bot commented Jul 2, 2026

nf-core pipelines lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

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`nf-core pipelines lint` overall result: Failed ❌