Template update for nf-core/tools version 2.12 #416

svarona · 2024-02-09T12:40:22Z

PR checklist

github-actions · 2024-02-09T12:42:22Z

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

Posted for pipeline commit 7d7571f

+| ✅ 176 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

files_exist - File not found: assets/multiqc_config.yml
files_exist - File not found: conf/igenomes.config
files_exist - File not found: lib/WorkflowViralrecon.groovy
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
system_exit - System.exit in nanopore.nf: System.exit(1) [line 237]

❔ Tests ignored:

files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
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/ci.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-viralrecon_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-viralrecon_logo_light.png
files_exist - File found: docs/images/nf-core-viralrecon_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: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
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: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: .nf-core.yaml
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: .github/workflows/push_dockerhub.yml
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: docs/images/nf-core-viralrecon_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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/Workflow.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
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: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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 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 ends in dev: 2.7.0dev
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.primer_left_suffix= _LEFT
nextflow_config - Config default value correct: params.primer_right_suffix= _RIGHT
nextflow_config - Config default value correct: params.min_barcode_reads= 100
nextflow_config - Config default value correct: params.min_guppyplex_reads= 10
nextflow_config - Config default value correct: params.artic_minion_caller= nanopolish
nextflow_config - Config default value correct: params.artic_minion_aligner= minimap2
nextflow_config - Config default value correct: params.asciigenome_read_depth= 50
nextflow_config - Config default value correct: params.asciigenome_window_size= 50
nextflow_config - Config default value correct: params.freyja_db_name= freyja_db
nextflow_config - Config default value correct: params.freyja_repeats= 100
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.kraken2_db= s3://ngi-igenomes/test-data/viralrecon/kraken2_human.tar.gz
nextflow_config - Config default value correct: params.kraken2_db_name= human
nextflow_config - Config default value correct: params.kraken2_assembly_host_filter= true
nextflow_config - Config default value correct: params.consensus_caller= bcftools
nextflow_config - Config default value correct: params.min_mapped_reads= 1000
nextflow_config - Config default value correct: params.skip_markduplicates= true
nextflow_config - Config default value correct: params.assemblers= spades
nextflow_config - Config default value correct: params.spades_mode= rnaviral
nextflow_config - Config default value correct: params.skip_plasmidid= true
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.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
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
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/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-viralrecon_logo_light.png matches the template
files_unchanged - docs/images/nf-core-viralrecon_logo_light.png matches the template
files_unchanged - docs/images/nf-core-viralrecon_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
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.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: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (444 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
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.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'

Run details

nf-core/tools version 2.12.1
Run at 2024-02-16 08:01:46

maxulysse · 2024-02-15T14:35:39Z

README.md

+    <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-viralrecon_logo_dark.png">
+    <img alt="nf-core/viralrecon" src="docs/images/nf-core-viralrecon_logo_light.png">
+  </picture>
+</h1>


Suggested change

</h1>

</h1>

Need an extra line not to break the badges

maxulysse · 2024-02-15T14:37:04Z

package-lock.json

where is this file coming from?

I actually don't know, I thought it came from the template but it doesn't seem to. Should I remove this one and the other one?

I don't think it's from the TEMPLATE indeed, cf:

https://github.com/nf-core/viralrecon/tree/TEMPLATE

https://github.com/nf-core/tools/tree/dev/nf_core/pipeline-template

So I'd go for removal if you're unsure why these files are here

maxulysse · 2024-02-15T14:37:08Z

package.json

where is this file coming from?

maxulysse

LGTM

nf-core-bot and others added 12 commits January 29, 2024 15:13

Template update for nf-core/tools version 2.12

c27f216

Merge branch 'nf-core-template-merge-2.12' into dev_template

a83efe1

Updated modules

13e7afa

Fixed linting

a266630

Fixed left-padding spaces

8a88cbd

Fixed prettier

f5eff26

Fixed prettier

019d9ec

unset changelog indent style

247132a

fixed prettier

c7c80ed

fixed prettier

ea05e7c

fixed prettier again

8f3ee29

Fixed logo linting

96b9f4d

svarona added 4 commits February 14, 2024 13:23

Added free some space to Test workflow parameters

854ed2d

Added Free some space to Run pipeline with test data

9562493

Added publish_dir_mode link to free some space

498b080

Added jlumbroso free space

aa8e4e3

maxulysse reviewed Feb 15, 2024

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where is this file coming from?

svarona added 2 commits February 16, 2024 08:59

Removed empty files

dd193f5

Added extra line to see badges

7d7571f

maxulysse approved these changes Feb 16, 2024

View reviewed changes

svarona mentioned this pull request Feb 16, 2024

Important! Template update for nf-core/tools v2.12 #414

Closed

svarona merged commit 1683739 into nf-core:dev Feb 16, 2024
22 checks passed

svarona deleted the dev_template branch April 8, 2024 09:03

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Template update for nf-core/tools version 2.12 #416

Template update for nf-core/tools version 2.12 #416

svarona commented Feb 9, 2024 •

edited

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github-actions bot commented Feb 9, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse Feb 15, 2024

maxulysse Feb 15, 2024

svarona Feb 15, 2024

maxulysse Feb 15, 2024

maxulysse Feb 15, 2024

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Template update for nf-core/tools version 2.12 #416

Template update for nf-core/tools version 2.12 #416

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svarona commented Feb 9, 2024 • edited Loading

PR checklist

github-actions bot commented Feb 9, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse Feb 15, 2024

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maxulysse Feb 15, 2024

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svarona Feb 15, 2024

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svarona commented Feb 9, 2024 •

edited

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github-actions bot commented Feb 9, 2024 •

edited

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