Important! Template update for nf-core/tools v3.3.2 by nf-core-bot · Pull Request #170 · nf-core/genomeassembler

nf-core-bot · 2025-07-08T11:38:34Z

Version 3.3.2 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.3.2 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.3.2 release page.

nextflow.config

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

nf-test.config

github-actions · 2025-07-11T08:22:49Z

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

Posted for pipeline commit 8fa5ba7

+| ✅ 201 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.1.0
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: assets/sendmail_template.txt
files_exist - File is ignored: assets/multiqc_config.yml
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
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: 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/nf-core-genomeassembler_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-genomeassembler_logo_light.png
files_exist - File found: docs/images/nf-core-genomeassembler_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: 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-genomeassembler_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/WorkflowGenomeassembler.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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 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 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.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.use_ref= true
nextflow_config - Config default value correct: params.jellyfish= true
nextflow_config - Config default value correct: params.kmer_length= 21
nextflow_config - Config default value correct: params.assembler= flye
nextflow_config - Config default value correct: params.flye_mode= --nano-hq
nextflow_config - Config default value correct: params.trim_short_reads= true
nextflow_config - Config default value correct: params.meryl_k= 21
nextflow_config - Config default value correct: params.merqury= true
nextflow_config - Config default value correct: params.qc_reads= ONT
nextflow_config - Config default value correct: params.busco= true
nextflow_config - Config default value correct: params.busco_lineage= brassicales_odb10
nextflow_config - Config default value correct: params.quast= true
nextflow_config - Config default value correct: params.lift_annotations= true
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-genomeassembler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-genomeassembler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-genomeassembler_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: 24.10.5, Config: 24.10.5
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
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: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: awstest.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: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
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: 3.3.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.3.2
Run at 2025-07-11 08:53:28

* Template update for nf-core/tools version 3.2.1 * Template update for nf-core/tools version 3.3.1 * Template update for nf-core/tools version 3.3.2 * fix nf-core.yml * Update nextflow.config Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io> * restore nf-test.config * restore ci * remove duplicated line * add nftignore * add tests/nextflow.config * exlcude svg from pre-commit * bump CI NXF_VER * bump CI NXF_VER * end of file * fix linting * pull request template * pull request template --------- Co-authored-by: Niklas Schandry <niklas@bio.lmu.de> Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

nf-core-bot and others added 5 commits April 30, 2025 12:26

Template update for nf-core/tools version 3.2.1

4e77b09

Template update for nf-core/tools version 3.3.1

e8ff0b9

Template update for nf-core/tools version 3.3.2

252486f

Merge branch 'dev' into nf-core-template-merge-3.3.2

7969333

fix nf-core.yml

f22e83c

maxulysse reviewed Jul 11, 2025

View reviewed changes

nextflow.config Outdated Show resolved Hide resolved

Update nextflow.config

1b69e2a

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

maxulysse reviewed Jul 11, 2025

View reviewed changes

nf-test.config Show resolved Hide resolved

nschan added 12 commits July 11, 2025 08:28

restore nf-test.config

75836d6

restore ci

6d91b3f

remove duplicated line

28cea6d

add nftignore

f8217fd

add tests/nextflow.config

844d098

exlcude svg from pre-commit

c7a6e6b

bump CI NXF_VER

ce0e258

bump CI NXF_VER

2a6fbf1

end of file

065b6b2

fix linting

798867e

pull request template

e306f9a

pull request template

8fa5ba7

maxulysse approved these changes Jul 11, 2025

View reviewed changes

nschan merged commit 0d30fd1 into dev Jul 11, 2025
22 checks passed

nschan deleted the nf-core-template-merge-3.3.2 branch July 11, 2025 09:06

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Important! Template update for nf-core/tools v3.3.2#170

Important! Template update for nf-core/tools v3.3.2#170
nschan merged 18 commits intodevfrom
nf-core-template-merge-3.3.2

nf-core-bot commented Jul 8, 2025

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edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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nf-core-bot commented Jul 8, 2025

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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Reviewers

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github-actions bot commented Jul 11, 2025 •

edited

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