Make `utils_nfcore_<pipeline>_pipeline` subworkflow nf-core linting compliant or don't lint file
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bug
linting
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of the bug
We should ensure that everything in the pipeline template is nf-core/tools linting compliant.
Currently, the local subworklow that comes with the template: utils_nfcore_<pipeline>_pipeline, violates multple linting rules, mainly:
- main_nf_include_versions (presumably will disappear once topics transition completed)
- meta_yml_exists
Meaning every pipeline gets warnings over something that a developer did not explicitly install.
We should either make a meta.yml file and/or add versions, or exclude the local subworkflow from all subworkflow linting.
Command used and terminal output
james@bionb103:~/git/nf-core/taxprofiler (local-subwf-nf-core-ling-compliance-yaml)$ nf-core pipelines lint
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 3.5.2 - https://nf-co.re
INFO Testing pipeline: .
Running lint checks ━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 27 » files_unchangedINFO Saving metadata file to '/tmp/tmpi6_jq06h/nf-core-taxprofiler'
╭─ [?] 3 Pipeline Tests Ignored ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ files_exist: File is ignored: conf/igenomes.config │
│ files_exist: File is ignored: conf/igenomes_ignored.config │
│ files_unchanged: File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [!] 57 Module Test Warnings ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ ╷ ╷ │
│ Module name │ File path │ Test message │
│╶────────────────────────────────┼────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────╴│
│ adapterremoval │ modules/nf-core/adapterremoval │ module_version: New version available │
│ bbmap/bbduk │ modules/nf-core/bbmap/bbduk │ module_version: New version available │
│ bowtie2/align │ modules/nf-core/bowtie2/align │ module_version: New version available │
│ bowtie2/build │ modules/nf-core/bowtie2/build │ module_version: New version available │
│ bracken/bracken │ modules/nf-core/bracken/bracken │ module_version: New version available │
│ bracken/combinebrackenoutputs │ modules/nf-core/bracken/combinebrackenoutputs │ module_version: New version available │
│ cat/fastq │ modules/nf-core/cat/fastq │ module_version: New version available │
│ centrifuge/centrifuge │ modules/nf-core/centrifuge/centrifuge │ module_version: New version available │
│ centrifuge/kreport │ modules/nf-core/centrifuge/kreport │ module_version: New version available │
│ diamond/blastx │ modules/nf-core/diamond/blastx │ module_version: New version available │
│ falco │ modules/nf-core/falco │ module_version: New version available │
│ fastp │ modules/nf-core/fastp │ module_version: New version available │
│ fastqc │ modules/nf-core/fastqc │ module_version: New version available │
│ filtlong │ modules/nf-core/filtlong │ module_version: New version available │
│ ganon/classify │ modules/nf-core/ganon/classify │ module_version: New version available │
│ ganon/report │ modules/nf-core/ganon/report │ module_version: New version available │
│ ganon/table │ modules/nf-core/ganon/table │ module_version: New version available │
│ gunzip │ modules/nf-core/gunzip │ module_version: New version available │
│ kaiju/kaiju │ modules/nf-core/kaiju/kaiju │ module_version: New version available │
│ kaiju/kaiju2krona │ modules/nf-core/kaiju/kaiju2krona │ module_version: New version available │
│ kaiju/kaiju2table │ modules/nf-core/kaiju/kaiju2table │ module_version: New version available │
│ kmcp/profile │ modules/nf-core/kmcp/profile │ module_version: New version available │
│ kmcp/search │ modules/nf-core/kmcp/search │ module_version: New version available │
│ kraken2/kraken2 │ modules/nf-core/kraken2/kraken2 │ module_version: New version available │
│ krakentools/combinekreports │ modules/nf-core/krakentools/combinekreports │ module_version: New version available │
│ krakentools/kreport2krona │ modules/nf-core/krakentools/kreport2krona │ module_version: New version available │
│ krona/ktimporttaxonomy │ modules/nf-core/krona/ktimporttaxonomy │ module_version: New version available │
│ krona/ktimporttext │ modules/nf-core/krona/ktimporttext │ module_version: New version available │
│ malt/run │ modules/nf-core/malt/run │ module_version: New version available │
│ megan/rma2info │ modules/nf-core/megan/rma2info │ module_version: New version available │
│ melon │ modules/nf-core/melon │ module_version: New version available │
│ metacache/query │ modules/nf-core/metacache/query │ module_version: New version available │
│ metaphlan/mergemetaphlantables │ modules/nf-core/metaphlan/mergemetaphlantables │ module_version: New version available │
│ metaphlan/metaphlan │ modules/nf-core/metaphlan/metaphlan │ module_version: New version available │
│ minimap2/align │ modules/nf-core/minimap2/align │ module_version: New version available │
│ minimap2/index │ modules/nf-core/minimap2/index │ module_version: New version available │
│ motus/merge │ modules/nf-core/motus/merge │ module_version: New version available │
│ motus/preplong │ modules/nf-core/motus/preplong │ module_version: New version available │
│ motus/profile │ modules/nf-core/motus/profile │ module_version: New version available │
│ multiqc │ modules/nf-core/multiqc │ module_version: New version available │
│ nanoq │ modules/nf-core/nanoq │ module_version: New version available │
│ nonpareil/curve │ modules/nf-core/nonpareil/curve │ module_version: New version available │
│ nonpareil/nonpareil │ modules/nf-core/nonpareil/nonpareil │ module_version: New version available │
│ nonpareil/nonpareilcurvesr │ modules/nf-core/nonpareil/nonpareilcurvesr │ module_version: New version available │
│ nonpareil/set │ modules/nf-core/nonpareil/set │ module_version: New version available │
│ porechop/abi │ modules/nf-core/porechop/abi │ module_version: New version available │
│ porechop/porechop │ modules/nf-core/porechop/porechop │ module_version: New version available │
│ samtools/fastq │ modules/nf-core/samtools/fastq │ module_version: New version available │
│ samtools/index │ modules/nf-core/samtools/index │ module_version: New version available │
│ samtools/stats │ modules/nf-core/samtools/stats │ module_version: New version available │
│ samtools/view │ modules/nf-core/samtools/view │ module_version: New version available │
│ sylph/profile │ modules/nf-core/sylph/profile │ module_version: New version available │
│ sylphtax/merge │ modules/nf-core/sylphtax/merge │ module_version: New version available │
│ sylphtax/taxprof │ modules/nf-core/sylphtax/taxprof │ module_version: New version available │
│ taxpasta/merge │ modules/nf-core/taxpasta/merge │ module_version: New version available │
│ taxpasta/standardise │ modules/nf-core/taxpasta/standardise │ module_version: New version available │
│ untar │ modules/nf-core/untar │ module_version: New version available │
│ ╵ ╵ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [!] 14 Subworkflow Test Warnings ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ ╷ ╷ │
│ Subworkflow name │ File path │ Test message │
│╶───────────────────────────────────┼───────────────────────────────────────────────────────────────┼────────────────────────────────────────────────────────────────────────────────────────╴│
│ utils_nfcore_taxprofiler_pipeline │ subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf │ main_nf_include_used: Included component 'paramsHelp' not used in main.nf │
│ longread_hostremoval │ subworkflows/local/longread_hostremoval/main.nf │ main_nf_include_versions: Included component 'SAMTOOLS_STATS' versions are not added in │
│ │ │ main.nf. Can be ignored if the module is using topic channels │
│ longread_hostremoval │ subworkflows/local/longread_hostremoval/main.nf │ main_nf_include_versions: Included component 'SAMTOOLS_VIEW' versions are not added in │
│ │ │ main.nf. Can be ignored if the module is using topic channels │
│ shortread_adapterremoval │ subworkflows/local/shortread_adapterremoval/main.nf │ main_nf_include_versions: Included component 'CAT_FASTQ' versions are not added in │
│ │ │ main.nf. Can be ignored if the module is using topic channels │
│ shortread_hostremoval │ subworkflows/local/shortread_hostremoval/main.nf │ main_nf_include_versions: Included component 'SAMTOOLS_STATS' versions are not added in │
│ │ │ main.nf. Can be ignored if the module is using topic channels │
│ utils_nfcore_taxprofiler_pipeline │ subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf │ main_nf_include_versions: Included component 'UTILS_NEXTFLOW_PIPELINE' versions are not │
│ │ │ added in main.nf. Can be ignored if the module is using topic channels │
│ utils_nfcore_taxprofiler_pipeline │ subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf │ main_nf_include_versions: Included component 'UTILS_NFCORE_PIPELINE' versions are not │
│ │ │ added in main.nf. Can be ignored if the module is using topic channels │
│ utils_nfcore_taxprofiler_pipeline │ subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf │ main_nf_include_versions: Included component 'UTILS_NFSCHEMA_PLUGIN' versions are not │
│ │ │ added in main.nf. Can be ignored if the module is using topic channels │
│ utils_nfcore_taxprofiler_pipeline │ subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf │ main_nf_include_versions: Included component 'completionEmail' versions are not added │
│ │ │ in main.nf. Can be ignored if the module is using topic channels │
│ utils_nfcore_taxprofiler_pipeline │ subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf │ main_nf_include_versions: Included component 'completionSummary' versions are not added │
│ │ │ in main.nf. Can be ignored if the module is using topic channels │
│ utils_nfcore_taxprofiler_pipeline │ subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf │ main_nf_include_versions: Included component 'paramsHelp' versions are not added in │
│ │ │ main.nf. Can be ignored if the module is using topic channels │
│ utils_nfcore_taxprofiler_pipeline │ subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf │ main_nf_include_versions: Included component 'paramsSummaryMap' versions are not added │
│ │ │ in main.nf. Can be ignored if the module is using topic channels │
│ utils_nfcore_taxprofiler_pipeline │ subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf │ main_nf_include_versions: Included component 'samplesheetToList' versions are not added │
│ │ │ in main.nf. Can be ignored if the module is using topic channels │
│ utils_nfcore_taxprofiler_pipeline │ subworkflows/local/utils_nfcore_taxprofiler_pipeline/meta.yml │ meta_yml_exists: Subworkflow meta.yml does not exist │
│ ╵ ╵ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
System information
No response
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Run nf-core pipelines lint on the pipeline template and inspect the utils_nfcore_<pipeline>_pipeline local subworkflow against the main_nf_include_versions and meta_yml_exists checks. Done means the subworkflow is compliant, or the lint configuration excludes it without producing warnings for pipelines that use the template.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 65/100