Important! Template update for nf-core/tools v3.5.1 by nf-core-bot · Pull Request #89 · nf-core/coproid

nf-core-bot · 2025-11-20T09:31:34Z

Version 3.5.1 of nf-core/tools has just been released with updates to the nf-core template. For more details, check out the blog post: https://nf-co.re/blog/2025/tools-3_5_0

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.5.1 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 v3.5.1 release page.

Note

Since nf-core/tools 3.5.0, older template update PRs will not be automatically closed, but will remain open in your pipeline repository. Older template PRs will be automatically closed once a newer template PR has been merged.

github-actions · 2026-02-06T12:41:54Z

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

Posted for pipeline commit c57a5bc

+| ✅ 223 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   6 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.0.1
pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
schema_description - No description provided in schema for parameter: modules_testdata_base_path
schema_description - No description provided in schema for parameter: version

❔ Tests ignored:

files_unchanged - File ignored due to lint config: docs/images/nf-core-coproid_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-coproid_logo_dark.png

✅ 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-coproid_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-coproid_logo_light.png
files_exist - File found: docs/images/nf-core-coproid_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-coproid_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/WorkflowCoproid.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 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.multiqc_title= coproid
nextflow_config - Config default value correct: params.file_prefix= coproid
nextflow_config - Config default value correct: params.taxa_sqlite= [:]/genomics/prokaryotes/metagenome/taxonomy/misc/taxa_sqlite.xz
nextflow_config - Config default value correct: params.taxa_sqlite_traverse_pkl= [:]/genomics/prokaryotes/metagenome/taxonomy/misc/taxa_sqlite_traverse.pkl
nextflow_config - Config default value correct: params.sam2lca_acc2tax= adnamap
nextflow_config - Config default value correct: params.sam2lca_identity= 0.9
nextflow_config - Config default value correct: params.igenomes_ignore= true
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/
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/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-coproid_logo_light.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: 25.04.0, Config: 25.04.0
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: 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: template_version_comment.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 - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - SOURCEPREDICT found in conf/modules.config and Nextflow scripts.
modules_config - SAM2LCA_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - PYDAMAGE_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - DAMAGEPROFILER_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - PYDAMAGE_ANALYZE found in conf/modules.config and Nextflow scripts.
modules_config - SAM2LCA_PREPDB found in conf/modules.config and Nextflow scripts.
modules_config - SAM2LCA_ANALYZE found in conf/modules.config and Nextflow scripts.
modules_config - QUARTONOTEBOOK found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_ACC2TAX found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN_PARSE found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_ found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
modules_config - XZ_DECOMPRESS 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: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-02-11 12:49:31

jfy133 · 2026-02-06T12:49:32Z

@nf-core-bot fix linting

…roid into nf-core-template-merge-3.5.1

jfy133 · 2026-02-06T14:02:19Z

@nf-core-bot fix linting

…roid into nf-core-template-merge-3.5.1

jfy133 · 2026-02-11T11:06:15Z

@nf-core-bot fix linting

…roid into nf-core-template-merge-3.5.1

jfy133 · 2026-02-11T12:03:01Z

@nf-core-bot fix linting

…roid into nf-core-template-merge-3.5.1

MeriamOs

Tested on HPC and runs successfully to completion. Fixed a previous issue with sam2lca and now runs with the newest Nextflow version!

nf-core-bot and others added 9 commits April 30, 2025 12:26

Template update for nf-core/tools version 3.2.1

55ee070

Template update for nf-core/tools version 3.3.1

0a0063d

Template update for nf-core/tools version 3.3.2

f6e0d6f

Template update for nf-core/tools version 3.4.1

da41054

Template update for nf-core/tools version 3.5.1

1c17fa4

Merge branch 'dev' into nf-core-template-merge-3.5.1

5426df9

More updates

d51a4f3

Try fix mqc linitng

de17f2a

Update samt2lca so pipeline executes

717650f

nf-core-bot and others added 3 commits February 6, 2026 12:49

[automated] Fix code linting

67f3352

Add basic snapshot - file names only no md5sums

8e298b2

Merge branch 'nf-core-template-merge-3.5.1' of github.com:nf-core/cop…

29ad3f6

…roid into nf-core-template-merge-3.5.1

nf-core-bot and others added 3 commits February 6, 2026 14:02

[automated] Fix code linting

c5823bb

Repair sourcepredict patch

5c0201b

Merge branch 'nf-core-template-merge-3.5.1' of github.com:nf-core/cop…

cf893af

…roid into nf-core-template-merge-3.5.1

nf-core-bot and others added 4 commits February 11, 2026 11:06

[automated] Fix code linting

e21cedd

Add missing input and update patch

95bf7c2

Merge branch 'nf-core-template-merge-3.5.1' of github.com:nf-core/cop…

0408f3e

…roid into nf-core-template-merge-3.5.1

Final port of patched changes

a81bdaf

nf-core-bot and others added 3 commits February 11, 2026 12:03

[automated] Fix code linting

027147f

Update snapshot

42d47f3

Merge branch 'nf-core-template-merge-3.5.1' of github.com:nf-core/cop…

7c6bbab

…roid into nf-core-template-merge-3.5.1

jfy133 mentioned this pull request Feb 11, 2026

Minor corrections in README file #94

Merged

4 tasks

jfy133 added 2 commits February 11, 2026 13:47

Add tools update to CHANGELOG and retrieve old pipeline Chagnelog

642cce2

Add tools update to CHANGELOG and retrieve old pipeline Chagnelog

c57a5bc

MeriamOs self-requested a review February 15, 2026 22:06

MeriamOs approved these changes Feb 15, 2026

View reviewed changes

MeriamOs merged commit 1c63bc8 into dev Feb 15, 2026
11 checks passed

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Important! Template update for nf-core/tools v3.5.1 - #89

Important! Template update for nf-core/tools v3.5.1#89
MeriamOs merged 24 commits into
devfrom
nf-core-template-merge-3.5.1

nf-core-bot commented Nov 20, 2025

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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nf-core-bot commented Nov 20, 2025

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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jfy133 commented Feb 6, 2026

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jfy133 commented Feb 6, 2026

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jfy133 commented Feb 11, 2026

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jfy133 commented Feb 11, 2026

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github-actions Bot commented Feb 6, 2026 •

edited

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