Release PR: 1.2.0 by jfy133 · Pull Request #59 · nf-core/demo

jfy133 · 2026-06-24T07:43:01Z

PR checklist

… the config tutorial

… into add-unlabelled-local-module

Important! Template update for nf-core/tools v4.0.2

… into add-unlabelled-local-module

Add small local module

…ersion-bump-for-1.2

Bump version for release

github-actions · 2026-06-24T07:44:52Z

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

Posted for pipeline commit c193351

+| ✅ 209 tests passed       |+
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/demo/demo/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
_
included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

✅ 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/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-demo_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/CONTRIBUTING.md
files_exist - File found: docs/images/nf-core-demo_logo_light.png
files_exist - File found: docs/images/nf-core-demo_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: conf/igenomes.config
files_exist - File found: conf/igenomes_ignored.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-demo_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/WorkflowDemo.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.igenomes_base= s3://ngi-igenomes/igenomes/
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/
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/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-demo_logo_light.png matches the template
files_unchanged - docs/images/nf-core-demo_logo_light.png matches the template
files_unchanged - docs/images/nf-core-demo_logo_dark.png matches the template
files_unchanged - docs/README.md 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
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: 25.10.4, Config: 25.10.4
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
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: 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: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.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_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 - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - SEQTK_TRIM found in conf/modules.config and Nextflow scripts.
modules_config - COWPY found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC 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: 4.0.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
container_configs - conf/containers_conda_lock_files_amd64.config is up to date
container_configs - conf/containers_conda_lock_files_arm64.config is up to date
container_configs - conf/containers_docker_amd64.config is up to date
container_configs - conf/containers_docker_arm64.config is up to date
container_configs - conf/containers_singularity_https_amd64.config is up to date
container_configs - conf/containers_singularity_https_arm64.config is up to date
container_configs - conf/containers_singularity_oras_amd64.config is up to date
container_configs - conf/containers_singularity_oras_arm64.config is up to date
version_consistency - Version tags are consistent: manifest.version = 1.2.0, nfcore_yml.version = 1.2.0

Run details

nf-core/tools version 4.0.2
Run at 2026-06-24 09:26:12

maxulysse

minor comments

charles-plessy

Looks good to me!

jfy133 · 2026-06-24T10:09:36Z

Thanks @maxulysse @charles-plessy @matthdsm !

ewels and others added 30 commits January 30, 2026 13:46

Verison bump: 1.2.0dev

cf41656

Merge pull request #52 from nf-core/1.2.0dev-version-bump

0dc6156

Changing test_full.config to use the larger test dataset from viralrecon

1ed4207

updated changelog

58ec89b

Merge branch 'dev' into test_full_update

8b48bb6

Merge pull request #54 from nf-core/test_full_update

ed969ce

Template update for nf-core/tools version 4.0.0

b417089

Template update for nf-core/tools version 4.0.2

44ef7ed

Add small local module with no tags to allow us to see changes during…

2f4add1

… the config tutorial

Update snapshot

b98299e

[automated] Fix code linting

33db43f

Replace variable fastfetch with cowpy, update docs and subwaymap

371c4bc

Merge branch 'add-unlabelled-local-module' of github.com:nf-core/demo…

2c879bd

… into add-unlabelled-local-module

[automated] Fix code linting

857def9

Fix links and add credits

c5a213d

Merge branch 'add-unlabelled-local-module' of github.com:nf-core/demo…

b9d6770

… into add-unlabelled-local-module

Merge template

a353442

REvert utils_nextflow_pipeline to template version

5d5a6d2

update citations

a47468b

Try bumping nf-test version

bec783e

Try latest version of nf-test

b194045

Try hardcoding outdir

db56678

Apply suggestion from @jfy133

ce64eb0

Apply suggestion from @jfy133

aa456e9

Update default.nf.test.snap

a8de803

Fix weird autoformatting things

027b032

Re-add comments

5a84f0a

Apply suggestion from @jfy133

d4d2c08

Merge pull request #56 from nf-core/nf-core-template-merge-4.0.2

86f84cc

Important! Template update for nf-core/tools v4.0.2

Merge branch 'dev' into add-unlabelled-local-module

9d1356a

nf-core-bot and others added 16 commits June 23, 2026 07:40

[automated] Fix code linting

f1c9560

Fix flattened line

28d70e7

Repair flattened lines

3050f9c

Linting clean up

9f01a85

Remove other flattening

7334a19

Apply suggestion from @jfy133

6534e64

Apply suggestion from @jfy133

cf44a98

Ungroup everything in SVG to see if renders nicely on github diff

2e6854c

Merge branch 'add-unlabelled-local-module' of github.com:nf-core/demo…

a6ac37c

… into add-unlabelled-local-module

Merge pull request #57 from nf-core/add-unlabelled-local-module

d238ec3

Add small local module

Bump version for release

9189b2f

Use real semvar

6516f65

Update .nf-core.yml

dab0bf3

Bump version

20936c5

Merge branch 'version-bump-for-1.2' of github.com:nf-core/demo into v…

eeafc48

…ersion-bump-for-1.2

Merge pull request #58 from nf-core/version-bump-for-1.2

1cdaa43

Bump version for release

jfy133 added 2 commits June 24, 2026 09:58

Fix cowpy conda env file name

9f1bdd3

Merge branch 'dev' of github.com:nf-core/demo into dev

e692add

maxulysse reviewed Jun 24, 2026

View reviewed changes

Comment thread conf/modules.config

maxulysse reviewed Jun 24, 2026

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Comment thread conf/test.config Outdated

maxulysse approved these changes Jun 24, 2026

View reviewed changes

jfy133 added 2 commits June 24, 2026 10:16

Fix tests executing and remove debuggin parameter

6262abd

Remove other temporary ebugging line

9b2c555

matthdsm approved these changes Jun 24, 2026

View reviewed changes

charles-plessy approved these changes Jun 24, 2026

View reviewed changes

jfy133 commented Jun 24, 2026

View reviewed changes

Comment thread CHANGELOG.md Outdated

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c193351

jfy133 merged commit 32893af into master Jun 24, 2026
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Release PR: 1.2.0#59

Release PR: 1.2.0#59
jfy133 merged 51 commits into
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jfy133 commented Jun 24, 2026

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github-actions Bot commented Jun 24, 2026 •

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jfy133 commented Jun 24, 2026

PR checklist

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github-actions Bot commented Jun 24, 2026 • 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 passed:

Run details

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github-actions Bot commented Jun 24, 2026 •

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