files_exist

PipelineLint.files_exist() → Dict[str, List[str]]

Checks a given pipeline directory for required files.

Iterates through the pipeline’s directory content and checks that specified files are either present or absent, as required.

Note

This test raises an AssertionError if neither nextflow.config or main.nf are found. If these files are not found then this cannot be a Nextflow pipeline and something has gone badly wrong. All lint tests are stopped immediately with a critical error message.

Files that must be present:

.gitattributes
.gitignore
.nf-core.yml
.editorconfig
.prettierignore
.prettierrc.yml
.github/.dockstore.yml
.github/CONTRIBUTING.md
.github/ISSUE_TEMPLATE/bug_report.yml
.github/ISSUE_TEMPLATE/config.yml
.github/ISSUE_TEMPLATE/feature_request.yml
.github/PULL_REQUEST_TEMPLATE.md
.github/workflows/branch.yml
.github/workflows/ci.yml
.github/workflows/linting_comment.yml
.github/workflows/linting.yml
[LICENSE, LICENSE.md, LICENCE, LICENCE.md]  # NB: British / American spelling
assets/email_template.html
assets/email_template.txt
assets/nf-core-PIPELINE_logo_light.png
assets/sendmail_template.txt
conf/modules.config
conf/test.config
conf/test_full.config
CHANGELOG.md
CITATIONS.md
CODE_OF_CONDUCT.md
docs/images/nf-core-PIPELINE_logo_light.png
docs/images/nf-core-PIPELINE_logo_dark.png
docs/output.md
docs/README.md
docs/usage.md
nextflow_schema.json
nextflow.config
README.md

Files that should be present:

main.nf
assets/multiqc_config.yml
conf/base.config
conf/igenomes.config
.github/workflows/awstest.yml
.github/workflows/awsfulltest.yml
ro-crate-metadata.json

Files that must not be present, due to being renamed or removed in the template:

.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/push_dockerhub.yml
.markdownlint.yml
.nf-core.yaml  # NB: Should be yml, not yaml
.yamllint.yml
bin/markdown_to_html.r
conf/aws.config
docs/images/nf-core-PIPELINE_logo.png
lib/Checks.groovy
lib/Completion.groovy
lib/NfcoreTemplate.groovy
lib/Utils.groovy
lib/Workflow.groovy
lib/WorkflowMain.groovy
lib/WorkflowPIPELINE.groovy
lib/nfcore_external_java_deps.jar
parameters.settings.json
pipeline_template.yml # saving information in .nf-core.yml
Singularity

Files that should not be present:

.travis.yml
Note

You can configure the nf-core pipelines lint tests to ignore any of these checks by setting the files_exist key as follows in your .nf-core.yml config file. For example:

lint: : files_exist: : - assets/multiqc_config.yml