nf-core pipeline lint gives cryptic prettier error message

[marrip]

Description of the bug

I created a custom pipeline with nf-core tools with minimal features and tried linting it. There were some issues with tests which were easy to fix, however, prettier fails and gives some cryptic error message (see below). I am not sure where this tmp folder comes from and what prettier is actually complaining about. Is it possible to turn it off for the nf-core lint process?

Command used and terminal output

$ nf-core pipelines lint -d nf-core-nextflow

                                      ,--./,-.
      ___     __   __   __   ___     /,-._.--~\ 
|\ | |__  __ /  ` /  \ |__) |__         }  {
| \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                      `._,._,'

nf-core/tools version 3.0.2 - https://nf-co.re

INFO Testing pipeline: nf-core-nextflow
Running lint checks ━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2 of 23 » files_unchanged CRITICAL Can't format ['/tmp/tmp9hyoxp1p/nf-core-nextflow/modules.json', '/tmp/tmp9hyoxp1p/nf-core-nextflow/tower.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/CHANGELOG.md', '/tmp/tmp9hyoxp1p/nf-core-nextflow/.prettierignore',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.editorconfig', '/tmp/tmp9hyoxp1p/nf-core-nextflow/conf', '/tmp/tmp9hyoxp1p/nf-core-nextflow/.gitattributes',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.prettierrc.yml', '/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/LICENSE', '/tmp/tmp9hyoxp1p/nf-core-nextflow/nextflow.config', '/tmp/tmp9hyoxp1p/nf-core-nextflow/assets',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github', '/tmp/tmp9hyoxp1p/nf-core-nextflow/modules', '/tmp/tmp9hyoxp1p/nf-core-nextflow/workflows',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.gitpod.yml', '/tmp/tmp9hyoxp1p/nf-core-nextflow/.nf-core.yml', '/tmp/tmp9hyoxp1p/nf-core-nextflow/docs',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.devcontainer', '/tmp/tmp9hyoxp1p/nf-core-nextflow/CITATIONS.md',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/CODE_OF_CONDUCT.md', '/tmp/tmp9hyoxp1p/nf-core-nextflow/.pre-commit-config.yaml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.gitignore', '/tmp/tmp9hyoxp1p/nf-core-nextflow/nextflow_schema.json',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/main.nf', '/tmp/tmp9hyoxp1p/nf-core-nextflow/README.md',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/conf/igenomes.config', '/tmp/tmp9hyoxp1p/nf-core-nextflow/conf/test_full.config',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/conf/igenomes_ignored.config', '/tmp/tmp9hyoxp1p/nf-core-nextflow/conf/test.config',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/conf/modules.config', '/tmp/tmp9hyoxp1p/nf-core-nextflow/conf/base.config',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/local', '/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/assets/schema_input.json', '/tmp/tmp9hyoxp1p/nf-core-nextflow/assets/adaptivecard.json',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/assets/methods_description_template.yml', '/tmp/tmp9hyoxp1p/nf-core-nextflow/assets/slackreport.json',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/assets/email_template.html', '/tmp/tmp9hyoxp1p/nf-core-nextflow/assets/nf-core-nextflow_logo_light.png',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/assets/samplesheet.csv', '/tmp/tmp9hyoxp1p/nf-core-nextflow/assets/multiqc_config.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/assets/sendmail_template.txt', '/tmp/tmp9hyoxp1p/nf-core-nextflow/assets/email_template.txt',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/.dockstore.yml', '/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/workflows',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/CONTRIBUTING.md', '/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/PULL_REQUEST_TEMPLATE.md',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/ISSUE_TEMPLATE', '/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/workflows/nextflow.nf', '/tmp/tmp9hyoxp1p/nf-core-nextflow/docs/usage.md',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/docs/images', '/tmp/tmp9hyoxp1p/nf-core-nextflow/docs/output.md',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/docs/README.md', '/tmp/tmp9hyoxp1p/nf-core-nextflow/.devcontainer/devcontainer.json',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/local/utils_nfcore_nextflow_pipeline',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfschema_plugin',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nextflow_pipeline',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfcore_pipeline',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/local/utils_nfcore_nextflow_pipeline/main.nf',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfschema_plugin/meta.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfschema_plugin/tests',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfschema_plugin/main.nf',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nextflow_pipeline/tests',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nextflow_pipeline/main.nf',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfcore_pipeline/tests',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfcore_pipeline/main.nf',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/workflows/awsfulltest.yml', '/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/workflows/linting.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/workflows/awstest.yml', '/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/workflows/linting_comment.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/workflows/template_version_comment.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/workflows/clean-up.yml', '/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/workflows/ci.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/workflows/branch.yml', '/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/workflows/fix-linting.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/workflows/release-announcements.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/workflows/download_pipeline.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/ISSUE_TEMPLATE/bug_report.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/ISSUE_TEMPLATE/feature_request.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/.github/ISSUE_TEMPLATE/config.yml', '/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/multiqc',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/fastqc', '/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/multiqc/meta.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/multiqc/environment.yml', '/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/multiqc/tests',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/multiqc/main.nf', '/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/fastqc/meta.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/fastqc/environment.yml', '/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/fastqc/tests',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/fastqc/main.nf',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/multiqc/tests/main.nf.test',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/multiqc/tests/tags.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/multiqc/tests/nextflow.config',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/multiqc/tests/main.nf.test.snap',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/fastqc/tests/main.nf.test',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/fastqc/tests/tags.yml',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/modules/nf-core/fastqc/tests/main.nf.test.snap',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/docs/images/nf-core-nextflow_logo_light.png',
'/tmp/tmp9hyoxp1p/nf-core-nextflow/docs/images/nf-core-nextflow_logo_dark.png'] because it has a syntax error.
prettier.................................................................Failed
- hook id: prettier
- exit code: 2

      ../../tmp/tmp9hyoxp1p/nf-core-nextflow/assets/adaptivecard.json: SyntaxError: Unexpected token (57:47)                                           
        55 |                                 {                                                                                                         
        56 |                                     "type": "FactSet",                                                                                    
      > 57 |                                     "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %> 
           |                                               ^                                                                                           
        58 |                                     ]                                                                                                     
        59 |                                 }                                                                                                         
        60 |                             ]                                                                                                             
                                                                                                                                                       
      ../../tmp/tmp9hyoxp1p/nf-core-nextflow/assets/slackreport.json: SyntaxError: Unexpected token (15:18)                                            
        13 |                     "short": false                                                                                                        
        14 |                 }                                                                                                                         
      > 15 |                 <%                                                                                                                        
           |                  ^                                                                                                                        
        16 |                     if (!success) { %>                                                                                                    
        17 |                     ,                                                                                                                     
        18 |                     {                                                                                                                     
     ../../tmp/tmp9hyoxp1p/nf-core-nextflow/assets/email_template.html                                                                                 
     ../../tmp/tmp9hyoxp1p/nf-core-nextflow/.nf-core.yml

System information

No response

[mirpedrol]

Hi @marrip,

We usually set prettier to skip these json files as they can not be linted by prettier. The .prettierignore file containing this:

email_template.html
adaptivecard.json
slackreport.json
.nextflow*
work/
data/
results/
.DS_Store
testing/
testing*
*.pyc
bin/

I guess you ticked off the feature of code linters? And that's why you don't have this file. When are you seeing this error? Because we don't run prettier with the nf-core pipelines lint command.