v2.0.0: First nf-core release #120

jmuhlich · 2025-10-20T14:07:17Z

First release!

These were added during some early testing and are no longer relevant.

Update affiliation and contact details for contributors

These modules' scripts didn't use "def" to define local variables as local so they were all part of the context and thus included in the task snapshot for nextflow task caching unnecessarily. This is mostly harmless but wasteful, however it did prevent some tasks from being usable with -resume since they have some local variables that Kryo serialization can't handle.

Make internal variables in local workflows local

Config updates

Add local mccellpose module as the default segmenter

Template update for nf-core/tools v3.4.1

Unify output filenames for segmenters and quantification

Update summary xml to include cycle number

The version was already 2.0.0 from the beginning, but I bumped "down" to 2.0.0-dev and then immediately back to 2.0.0 to make sure everything is up to date using the latest bump-version formatting.

Bump version 2.0.0

github-actions · 2025-10-20T14:09:38Z

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

Posted for pipeline commit 72e363c

+| ✅ 226 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
schema_lint - Parameter input not found in schema

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
nextflow_config - Config variable ignored: params.input
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-mcmicro_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-mcmicro_logo_light.png
files_exist - File found: docs/images/nf-core-mcmicro_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-mcmicro_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/WorkflowMcmicro.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: 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: 2.0.0
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.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/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' contains outdir parameter
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' contains outdir parameter
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' contains outdir parameter
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' contains outdir parameter
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' contains outdir parameter
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/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/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 - assets/nf-core-mcmicro_logo_light.png matches the template
files_unchanged - docs/images/nf-core-mcmicro_logo_light.png matches the template
files_unchanged - docs/images/nf-core-mcmicro_logo_dark.png 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_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awstest.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
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 - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - BASICPY found in conf/modules.config and Nextflow scripts.
modules_config - ASHLAR found in conf/modules.config and Nextflow scripts.
modules_config - BACKSUB 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 - MCCELLPOSE found in conf/modules.config and Nextflow scripts.
modules_config - MCQUANT found in conf/modules.config and Nextflow scripts.
modules_config - COREOGRAPH found in conf/modules.config and Nextflow scripts.
modules_config - BFTOOLS_SHOWINF found in conf/modules.config and Nextflow scripts.
modules_config - SCIMAP_MCMICRO 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 = 2.0.0, nfcore_yml.version = 2.0.0
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.4.1
Run at 2025-10-20 14:09:13

RobJY added 30 commits October 18, 2024 15:02

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jmuhlich and others added 29 commits October 9, 2025 11:59

Removed unused profiles and configs

0a73d4c

These were added during some early testing and are no longer relevant.

Fill out test_full config

ab971a3

Remove todo comments in various configs after review

c22e3ea

Merge pull request #109 from nf-core/fix-affiliation-orcid-fw

868abb3

Update affiliation and contact details for contributors

Merge pull request #112 from jmuhlich/local-modules-variable-scope

674f638

Make internal variables in local workflows local

Merge pull request #110 from jmuhlich/config-updates

ab85a06

Config updates

Add mccellpose module as default segmenter

6f8fff7

Update first batch of tests for mccellpose switch

8d0d608

Update remaining tests for mccellpose

832abc6

Update docs

53dd5f4

Update mccellpose container version

9072e6e

Fix markdown format

bee226c

Template update for nf-core/tools version 3.4.1

336fdf9

Update default test snapshot

12da455

Explain snapshot strategy for mccellpose module test

eba6a16

Merge pull request #113 from jmuhlich/mccellpose

ffde320

Add local mccellpose module as the default segmenter

Merge branch 'dev' into nf-core-template-merge-3.4.1

5fec7f1

Update tests and snapshots for new template

d2b4d7a

Merge pull request #115 from jmuhlich/nf-core-template-merge-3.4.1

2419dac

Template update for nf-core/tools v3.4.1

Unify output filenames for segmenters and quantification

6937b21

Update docs for new segmentation publish paths

49e23a3

Tighten mccellpose output mask path pattern

a19d4ae

Update summary xml to include cycle number

652ad18

Fix mccellpose stub output filename

6e7e8f0

Merge pull request #116 from jmuhlich/harmonize-output-names

a5a2489

Unify output filenames for segmenters and quantification

Merge pull request #117 from nf-core/AlexBarbera-summaryxmltag-1

d0121a6

Update summary xml to include cycle number

Bump version 2.0.0

4d9cade

The version was already 2.0.0 from the beginning, but I bumped "down" to 2.0.0-dev and then immediately back to 2.0.0 to make sure everything is up to date using the latest bump-version formatting.

Merge pull request #119 from jmuhlich/bump-version-2.0.0

72e363c

Bump version 2.0.0

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v2.0.0: First nf-core release #120

v2.0.0: First nf-core release #120

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jmuhlich commented Oct 20, 2025

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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v2.0.0: First nf-core release #120

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jmuhlich commented Oct 20, 2025

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github-actions bot commented Oct 20, 2025

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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