Crate wdl_lint

Lint rules for Workflow Description Language (WDL) documents.

Rules

This table documents all implemented wdl lint rules implemented on the main branch of the stjude-rust-labs/wdl repository. Note that the information may be out of sync with released packages.

Lint Rules

Name	Tags	Description
CallInputSpacing	Clarity, Spacing, Style	Ensures proper spacing for call inputs
CommandSectionIndentation	Clarity, Correctness, Spacing	Ensures consistent indentation (no mixed spaces/tabs) within command sections.
CommentWhitespace	Spacing	Ensures that comments are properly spaced.
ConciseInput	Style	Ensures concise input assignments are used (implicit binding when available).
ConsistentNewlines	Clarity, Style	Ensures that \n or \r\n newlines are used consistently within the file.
ContainerUri	Clarity, Portability	Ensures that the value for the container key in runtime/requirements sections is well-formed.
DeclarationName	Naming	Ensures declaration names do not redundantly include their type name.
DeprecatedObject	Deprecated	Ensures that the deprecated Object construct is not used.
DeprecatedPlaceholder	Deprecated	Ensures that the deprecated placeholder options construct is not used.
DoubleQuotes	Clarity, Style	Ensures that strings are defined using double quotes.
ElementSpacing	Spacing	Ensures proper blank space between elements
EndingNewline	Spacing, Style	Ensures that documents end with a single newline character.
ExpectedRuntimeKeys	Completeness, Deprecated	Ensures that runtime sections have the appropriate keys.
ExpressionSpacing	Spacing	Ensures that expressions are properly spaced.
HereDocCommands	Clarity	Ensures that tasks use heredoc syntax in command sections.
ImportPlacement	Clarity, Sorting	Ensures that imports are placed between the version statement and any document items.
ImportSorted	Clarity, Style	Ensures that imports are sorted lexicographically.
ImportWhitespace	Clarity, Spacing, Style	Ensures that there is no extraneous whitespace between or within imports.
InputName	Naming	Ensures input names are meaningful (e.g., not generic like ‘input’, ‘in’, or too short).
InputSorted	Clarity, Sorting, Style	Ensures that input declarations are sorted
KnownRules	Clarity	Ensures only known rules are used in lint directives.
LineWidth	Clarity, Spacing, Style	Ensures that lines do not exceed a certain width.
LintDirectiveFormatted	Clarity, Correctness	Ensures lint directives are correctly formatted.
LintDirectiveValid	Clarity, Correctness	Ensures lint directives are placed correctly to have the intended effect.
MatchingOutputMeta	Completeness	Ensures that each output field is documented in the meta section under meta.outputs.
MetaDescription	Completeness	Ensures the meta section contains a description key.
MetaKeyValueFormatting	Style	Ensures that metadata objects and arrays are properly spaced.
MetaSections	Clarity, Completeness	Ensures that tasks and workflows have the required meta and parameter_meta sections.
OutputName	Naming	Ensures output names are meaningful (e.g., not generic like ‘output’, ‘out’, or too short).
ParameterMetaMatched	Completeness, Sorting	Ensures that inputs have a matching entry in a parameter_meta section.
PascalCase	Clarity, Naming, Style	Ensures that structs are defined with PascalCase names.
PreambleCommentPlacement	Clarity	Ensures that documents have correct comments in the preamble.
PreambleFormatted	Clarity, Spacing, Style	Ensures that documents have correct whitespace in the preamble.
RedundantNone	Style, Clarity	Ensures optional inputs don’t have redundant None assignments.
RequirementsSection	Completeness, Portability	Ensures that >=v1.2 tasks have a requirements section.
RuntimeSection	Completeness, Portability	Ensures that <v1.2 tasks have a runtime section.
SectionOrdering	Sorting, Style	Ensures that sections within tasks and workflows are sorted.
ShellCheck	Correctness, Portability	Ensures that command sections are free of shellcheck diagnostics.
SnakeCase	Clarity, Naming, Style	Ensures that tasks, workflows, and variables are defined with snake_case names.
TodoComment	Completeness	Ensures that TODO statements are flagged for followup.
TrailingComma	Style	Ensures that lists and objects in meta have a trailing comma.
VersionStatementFormatted	Style	Ensures the version statement is correctly formatted.
Whitespace	Spacing, Style	Ensures that a document does not contain undesired whitespace.

Definitions

Definitions

WDL Document Structure

Preamble

The document preamble is defined as anything before the version declaration statement and the version declaration statement itself. Only comments and whitespace are permitted before the version declaration.

Comment Types

Lint Directives

Lint directives are special comments that begin with #@ except: followed by a comma-delimited list of rule IDs. These comments are used to disable specific lint rules for a section of the document. When a lint directive is encountered in the preamble, it will disable the specified rules for the entire document.

For example:

#@ except: LineWidth, CommentWhitespace

Preamble Comments

Preamble comments are special comments at the start of a WDL file that begin with double pound signs (##). These comments are used for documentation that doesn’t fit within any of the WDL-defined documentation elements (i.e., meta and parameter_meta sections). They may provide context for a collection of tasks or structs, or they may provide a high-level overview of a workflow. Preamble comments can be formatted as Markdown text.

For example:

## # FlagFilter
##
## A struct to represent the filtering flags used in various `samtools` commands.

Examples

An example of parsing a WDL document and linting it:

use wdl_lint::Linter;
use wdl_lint::analysis::Validator;
use wdl_lint::analysis::document::Document;

let mut validator = Validator::default();
validator.add_visitor(Linter::default());

Re-exports

pub use wdl_analysis as analysis;

pub use wdl_ast as ast;

Modules

rules

Module for the lint rules.

Structs

Linter

A visitor that runs linting rules.

TagSet

A set of lint tags.

UnknownTagError

An error for when an unknown tag is encountered.

Enums

Tag

A lint rule tag.

Constants

DEFINITIONS_TEXT

The definitions of WDL concepts and terminology used in the linting rules.

Traits

Rule

A trait implemented by lint rules.

Functions

find_nearest_rule

Finds the nearest rule ID to the given unknown rule ID, or None if no rule ID is close enough.

rules

Gets the default rule set.