main_nf

ModuleLint.main_nf(module: NFCoreComponent, fix_version: bool, registry: str, progress_bar: Progress) → tuple[list[str], list[str]]

Lint a main.nf module file

Can also be used to lint local module files, in which case failures will be reported as warnings.

The following checks are performed:

• main_nf_exists: The main.nf file must exist.
• deprecated_dsl2: The file must not contain deprecated DSL2 identifiers (initOptions, saveFiles, getSoftwareName, getProcessName, publishDir).
• main_nf_script_outputs: The process must have an output: block.
• main_nf_container: Container tags across the singularity, docker, and conda directives must reference the same software version. A warning is issued if they do not match.
• main_nf_script_shell: Exactly one of script:, shell:, or exec: blocks must be present.
• main_nf_shell_template: If a shell: block is used, it must call a template.
• main_nf_meta_output: If meta is present in the module inputs, it must also appear in at least one output channel.
• main_nf_version_topic: The module should emit software versions using a topic: versions output. A warning is issued if no such topic is found.
• main_nf_version_emit: The number of topic: versions outputs must equal the number of emit: outputs whose name starts with versions. A warning is issued if a legacy YAML-based versions emit is used instead of a topic output.