Update linting.yml

[DLBPointon]

Version is outdated

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[DLBPointon]

Version of node is now incompatible with editorconfig node-npm@3 is using 2.0.something, bumping to @4 should fix this.

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit eae9854

+| ✅ 108 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗  19 tests had warnings |!

❗ Test warnings:

• readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
• pipeline_todos - TODO string in README.md: TODO nf-core:
• pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
• pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
• pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
• pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
• pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
• pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
• pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
• pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
• 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
• pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
• pipeline_todos - TODO string in base.config: Check the defaults for all processes
• pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
• pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
• pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
• pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
• system_exit - System.exit in WorkflowAscc.groovy: System.exit(1) [line 18]
• nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

• files_exist - files_exist
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
• files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
• files_unchanged - File ignored due to lint config: assets/email_template.html
• files_unchanged - File ignored due to lint config: assets/nf-core-ascc_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-ascc_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-ascc_logo_dark.png
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/ascc/ascc/.github/workflows/awstest.yml
• multiqc_config - multiqc_config

✅ Tests passed:

• 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: 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 dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version ends in dev: 1.0dev
• 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.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.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.help= false
• nextflow_config - Config default value correct: params.version= false
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.plaintext_email= false
• nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
• nextflow_config - Config default value correct: params.monochrome_logs= false
• nextflow_config - Config default value correct: params.tracedir= results/pipeline_info/
• nextflow_config - Config default value correct: params.validate_params= true
• nextflow_config - Config default value correct: params.validationShowHiddenParams= false
• nextflow_config - Config default value correct: params.validationFailUnrecognisedParams= false
• nextflow_config - Config default value correct: params.validationLenientMode= false
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - assets/email_template.txt matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• files_unchanged - docs/README.md matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• readme - README Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (238 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/yaml'
• schema_params - Schema matched params returned from nextflow config
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: linting.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: branch.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'
• base_config - conf/base.config found and not ignored.
• base_config - BLAST_BLASTN_MOD found in conf/base.config and Nextflow scripts.
• base_config - DIAMOND_BLASTX found in conf/base.config and Nextflow scripts.
• base_config - KRAKEN2_KRAKEN2 found in conf/base.config and Nextflow scripts.
• base_config - MINIMAP2_ALIGN found in conf/base.config and Nextflow scripts.
• base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - SANGER_TOL_BTK found in conf/modules.config and Nextflow scripts.
• modules_config - AUTOFILTER_AND_CHECK_ASSEMBLY found in conf/modules.config and Nextflow scripts.
• modules_config - AUTOFILTER_AND_CHECK_ASSEMBLY found in conf/modules.config and Nextflow scripts.
• modules_config - GenIndicator found in conf/modules.config and Nextflow scripts.
• modules_config - ASCC_MERGE_TABLES found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_FASTA found in conf/modules.config and Nextflow scripts.
• modules_config - SEQKIT_SLIDING found in conf/modules.config and Nextflow scripts.
• modules_config - BLAST_MAKEBLASTDB found in conf/modules.config and Nextflow scripts.
• modules_config - DIAMOND_BLASTX found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_DEPTH found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
• modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
• modules_config - FCS_FCSADAPTOR_PROK found in conf/modules.config and Nextflow scripts.
• modules_config - FCS_FCSADAPTOR_EUK found in conf/modules.config and Nextflow scripts.
• modules_config - FCS_FCSADAPTOR_EUK found in conf/modules.config and Nextflow scripts.
• modules_config - SED_SED found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_ALIGN_SE found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_ALIGN_ILLUMINA found in conf/modules.config and Nextflow scripts.
• modules_config - NCBITOOLS_VECSCREEN found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_VECSCREEN_RESULTS found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline

Run details

• nf-core/tools version 2.14.1
• Run at 2024-10-07 21:34:34

[DLBPointon]

Hi @eeaunin and @muffato (in case this comes up in other pipelines)

I'm pinning the version of node as editorconfig 0.6.0 required >= 20.11.0 and the previous config was using 18 as default.

Could you approve this when you can please @eeaunin, this should then fix your docs branch which we can then merge to dev.