files_unchanged

PipelineLint.files_unchanged()

Checks that certain pipeline files are not modified from template output.

Iterates through the pipeline’s directory content and compares specified files against output from the template using the pipeline’s metadata. File content should not be modified / missing.

Files that must be unchanged:

.gitattributes
.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/linting_comment.yml
.github/workflows/linting.yml
assets/email_template.html
assets/email_template.txt
assets/nf-core-PIPELINE_logo_light.png
assets/sendmail_template.txt
CODE_OF_CONDUCT.md
docs/images/nf-core-PIPELINE_logo_light.png
docs/images/nf-core-PIPELINE_logo_dark.png
docs/README.md'
lib/NfcoreTemplate.groovy
['LICENSE', 'LICENSE.md', 'LICENCE', 'LICENCE.md'], # NB: British / American spelling

Files that can have additional content but must include the template contents:

.gitignore
.prettierignore
pyproject.toml

Files that need to be there or not based on a entry in nextflow config:

lib/nfcore_external_java_deps.jar # if config doesn't mention nf-validation
Note

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

lint:
  files_unchanged:
    - .github/workflows/branch.yml