v2.0.0: First nf-core release #120

jmuhlich · 2025-10-20T14:07:17Z

First release!

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 d20e677

+| ✅ 226 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 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 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/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' 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/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: 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.
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 2025-11-25 01:51:21

See https://nfcore.slack.com/archives/C050DNB6K5H/p1762184179238379 for details

Update to new runner size syntax

Refractored code structure to support nextflow version 24.10.x

(Except cellpose which we are deliberately holding back)

Old containers with an old version of glibc won't work when running under apptainer --nv on a newer host OS. This profile uses the more compatible but experimental --nvccli option instead for modules that are likely to be a problem. Developers running nf-test locally can select this profile as needed. Institutional configurations should be aware of the issue as well.

Module update

Changed summaryxml to be independent process

Include cycle number in relevant process tags

Updated for new summaryxml format

RobJY and others added 30 commits October 22, 2024 13:54

ci testing

8b6656e

ci testing

1d44216

ci testing

1057ed0

ci testing

ee21082

ci testing

b41e58a

ci testing

babe7a8

ci testing

feed6ae

ci testing

dd1fc80

ci testing

901fcb3

ci testing

e1a3878

ci testing

3b35a51

ci testing

dbe16ec

ci testing

16b06f1

ci testing

bbe5439

ci testing

9e37b56

ci testing

974cfd4

ci testing

185e2cf

ci testing

3ae2d89

ci testing

3de3581

merging template updates 3.0.2

0cebe0e

ci testing - basicpy & ashlar update

8e931c6

added nf-tests to ci and updated basipy and ashlar

092b889

forcing more nf-tests in ci

a0a98cd

update mesmer and added test param to not check conda channels

3b8797b

removed ineffective test param

65c6b2a

schema fix

1d2885b

removing forced tests for testing

a65f5aa

ran prettier

c31dced

added required final newline to ci.yml

d6ba5bd

testing detect-nf-test-changes fix

7cc158f

jmuhlich and others added 15 commits October 16, 2025 10:48

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

mashehu and others added 14 commits November 3, 2025 16:50

Update to new runner size syntax

79825db

See https://nfcore.slack.com/archives/C050DNB6K5H/p1762184179238379 for details

Refractored code structure to support nextflow version 24.10.x

e7fd280

Changed summaryxml to be independent process

a4a44b5

Merge pull request #123 from nf-core/mashehu-patch-1

3c86619

Update to new runner size syntax

Merge pull request #124 from AlexBarbera/backcompat

f916368

Refractored code structure to support nextflow version 24.10.x

Update modules to latest

535b4e8

(Except cellpose which we are deliberately holding back)

Merge pull request #125 from jmuhlich/module-update

f20ab98

Module update

Removed old code, reformated output and updated snapshot

82feab5

Merge pull request #126 from AlexBarbera/summaryscript

cc8ac47

Changed summaryxml to be independent process

Include cycle number in relevant process tags

ff4b561

Merge pull request #127 from jmuhlich/cycle-number-in-tags

3f32a6d

Include cycle number in relevant process tags

Updated for new summaryxml format

30cdb5f

Merge pull request #128 from AlexBarbera/testing

d20e677

Updated for new summaryxml format

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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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v2.0.0: First nf-core release #120

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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❔ Tests ignored:

✅ Tests passed:

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