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Run WDL linting on a WILDS module or pipeline and fix any issues found
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Based on SOC occupation classification
Create a new WILDS WDL module for a bioinformatics tool following project conventions
Create a new WILDS WDL pipeline that combines existing modules into a workflow
Add a new test data download task to the ww-testdata module for use in module/pipeline testruns
Draft a pull request description using the project's PR template
Run the testrun.wdl for a WILDS module or pipeline using sprocket or miniwdl
| 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 |
Run all available linting checks on $ARGUMENTS and fix any issues.
Check if $ARGUMENTS exists in modules/ or pipelines/:
modules/$ARGUMENTS/$ARGUMENTS.wdlpipelines/$ARGUMENTS/$ARGUMENTS.wdlmake lint NAME=$ARGUMENTS
This runs sprocket, miniwdl, and WOMtool linters.
If make targets aren't available, run sprocket directly:
make lint_sprocket NAME=$ARGUMENTS
For each lint error:
Known Sprocket exceptions (these are OK and won't cause failures):
Summarize what was found and fixed. If there are unfixable issues, explain why and suggest next steps.