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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?
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.
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
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
System information
No response
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