files_exist

PipelineLint.files_exist()

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
lib/NfcoreTemplate.groovy
lib/Utils.groovy
lib/WorkflowMain.groovy
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
lib/WorkflowPIPELINE.groovy
pyproject.toml

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

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

Files that should not be present:

.travis.yml

Files that must not be present if a certain entry is present in nextflow.config:

lib/nfcore_external_java_deps.jar # if "nf-validation" is in nextflow.config
Note

You can configure the nf-core 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