lint-module

name	lint-module
description	Run WDL linting on a WILDS module or pipeline and fix any issues found
argument-hint	<ww-name>
allowed-tools	Bash(make *), Read, Edit, Glob, Grep

Lint a WILDS WDL Module or Pipeline

Run all available linting checks on $ARGUMENTS and fix any issues.

Steps

1. Determine Module or Pipeline

Check if $ARGUMENTS exists in modules/ or pipelines/:

• Module: modules/$ARGUMENTS/$ARGUMENTS.wdl
• Pipeline: pipelines/$ARGUMENTS/$ARGUMENTS.wdl

2. Run Linting

make lint NAME=$ARGUMENTS

This runs sprocket, miniwdl, and WOMtool linters.

If make targets aren't available, run sprocket directly:

make lint_sprocket NAME=$ARGUMENTS

3. Fix Issues

For each lint error:

• Read the relevant WDL file
• Fix the issue following project conventions (see CLAUDE.md)
• Re-run linting to confirm the fix

Known Sprocket exceptions (these are OK and won't cause failures):

• TodoComment
• ContainerUri
• TrailingComma
• CommentWhitespace
• UnusedInput

4. Report Results

Summarize what was found and fixed. If there are unfixable issues, explain why and suggest next steps.