dev -> master for v1.1.0 release by ewels · Pull Request #51 · nf-core/demo

ewels · 2026-01-26T16:53:39Z

Changes to master for v1.1.0 release.

Resolves merge conflicts from template update: - Accept new devcontainer format (remoteUser/privileged instead of features) - Remove gitpod profile (replaced by codespaces/devcontainer) - Update MultiQC to 1.31 with new container images - Update Nextflow minimum version to 25.04.0 - Keep custom validation help/summary configuration - Keep seqtk/trim module - Preserve Zenodo DOI (10.5281/zenodo.12192442)

Resolves merge conflicts from template update: - Accept new Codespaces badge format (shields.io style) - Update template version badge to 3.5.1 - Update MultiQC to 1.32 with topic channels for versions - Update Channel to channel (lowercase) for strict Nextflow syntax - Preserve Zenodo DOI (10.5281/zenodo.12192442)

- Sync template files (PR template, linting workflow, logo images) - Add symlink for docs/CONTRIBUTING.md

Updated modules: - fastqc - multiqc (now 1.32) - seqtk/trim Updated subworkflows: - utils_nfcore_pipeline - utils_nfschema_plugin

Remove explicit .out.versions calls from FASTQC and SEQTK_TRIM modules as they now use topic channels (emit: versions_*, topic: versions). Versions are automatically collected via Channel.topic('versions').

- Remove version count (now using topic channels) - Remove BETA-multiqc.parquet (renamed) - Add llms-full.txt and multiqc.parquet (new MultiQC outputs)

- Fix linting.yml to use pip install instead of uv tool install - Add explicit pre-commit installation step - Sync PULL_REQUEST_TEMPLATE.md with template

github-actions · 2026-01-26T16:55:16Z

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

Posted for pipeline commit 60ebcaa

+| ✅ 203 tests passed       |+
!| ❗   1 tests had warnings |!

Details

❗ Test warnings:

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/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-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/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: 1.1.0
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.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/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-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: 25.10.2, Config: 25.10.2
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings 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_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.
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 - 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: 3.5.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 1.1.0, nfcore_yml.version = 1.1.0

Run details

nf-core/tools version 3.5.1
Run at 2026-01-26 16:54:56

nvnieuwk

LGTM

FloWuenne

LGTM2 🚀

nf-core-bot and others added 30 commits July 8, 2025 11:39

Template update for nf-core/tools version 3.3.2

5cd9b23

Template update for nf-core/tools version 3.4.1

35ef9b0

Template update for nf-core/tools version 3.5.1

ae46863

Sync RO-Crate metadata with README

e9e0e99

Fix nf-core lint failures

92d17ea

- Sync template files (PR template, linting workflow, logo images) - Add symlink for docs/CONTRIBUTING.md

Update nf-core modules and subworkflows

678f586

Updated modules: - fastqc - multiqc (now 1.32) - seqtk/trim Updated subworkflows: - utils_nfcore_pipeline - utils_nfschema_plugin

Fix topic channels for version handling

48c3dae

Remove explicit .out.versions calls from FASTQC and SEQTK_TRIM modules as they now use topic channels (emit: versions_*, topic: versions). Versions are automatically collected via Channel.topic('versions').

Update nf-test snapshot for MultiQC 1.33

e83f58a

- Remove version count (now using topic channels) - Remove BETA-multiqc.parquet (renamed) - Add llms-full.txt and multiqc.parquet (new MultiQC outputs)

Sync template files with nf-core/tools 3.5.1

b065772

- Fix linting.yml to use pip install instead of uv tool install - Add explicit pre-commit installation step - Sync PULL_REQUEST_TEMPLATE.md with template

Manually make mismatch files match the template

787f52a

Resolve jinja template strings

0240abe

More jinja tags. Go slow Phil, slow is smooth and smooth is fast.

28fc201

Merge pull request #49 from nf-core/template-strict-syntax-update

5e36ae6

Bump nf-schema and minimum nextflow

d483948

Update local utils_nfcore_demo_pipeline subworkflow and nextflow.config

d0cd83e

Update subworkflow calls

0b672c2

Update modules

3f526ba

Update subworkflows

b8e1aa8

Fix subworkflow call arguments again

8ec343c

Bump versions to 1.1.0

c58f97b

Fix typo: minimum nextflow version in the past, not the future

7189480

Update workflow logic for topics

2492995

Merge origin/dev into strict-syntax

439fe1c

Fix all warnings from 'nextflow lint'

757e290

Bump pipeline version again (not sure where that was lost)

7735616

Regenreate ROCrate JSON file

81c785d

Update MultiQC config bumped version

f44c427

Add mimetype to schema for params.input

2f6c251

ewels added 6 commits January 26, 2026 11:12

Update changelog for v1.1.0 release

61e83d8

Update nf-schema version and minimum Nextflow version

ad5b888

Pre-commit

0fde217

Bump minimum Nextflow version from 25.10.0 to 25.10.2

92ba342

Updated... something

c8a50ac

Merge pull request #50 from nf-core/strict-syntax

60ebcaa

ewels mentioned this pull request Jan 26, 2026

Pipeline updates (including strict syntax compliance) #50

Merged

nvnieuwk approved these changes Jan 27, 2026

View reviewed changes

FloWuenne approved these changes Jan 28, 2026

View reviewed changes

ewels merged commit 45904cb into master Jan 30, 2026
16 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

dev -> master for v1.1.0 release#51

dev -> master for v1.1.0 release#51
ewels merged 36 commits intomasterfrom
dev

ewels commented Jan 26, 2026

Uh oh!

github-actions bot commented Jan 26, 2026 •

edited

Loading

❗ Test warnings:

✅ Tests passed:

Run details

Uh oh!

nvnieuwk left a comment

Uh oh!

FloWuenne left a comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Conversation

ewels commented Jan 26, 2026

Uh oh!

github-actions bot commented Jan 26, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

Uh oh!

nvnieuwk left a comment

Choose a reason for hiding this comment

Uh oh!

FloWuenne left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

github-actions bot commented Jan 26, 2026 •

edited

Loading

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