Foundry
Agent Skill · cast

debug-cwl-workflow-output

Triage failing CWL run outputs; classify failure modes; propose fixes.

← All cast skills · Source mold →

Install with Claude Code

/plugin marketplace add galaxyproject/foundry
/plugin install foundry-skills@galaxy-workflow-foundry

Then invoke as:

/foundry-skills:debug-cwl-workflow-output

Install with Codex

codex plugin marketplace add galaxyproject/foundry
codex plugin add foundry-skills@galaxy-workflow-foundry

Then select with /skills or invoke explicitly as:

$debug-cwl-workflow-output

Skill Bundle

/ packaged cast
attached files
0
upfront
0
on demand
0
cast rev
n/a
validated
0

Produces: 1 artifact.

Consumes: 1 artifact.

Artifact Contract

/ skill handoff

Produces

cwl-workflow-debug-report

CWL failure-surface classification with captured run/job/output evidence and a recommended next step or reference-gap follow-up.

markdowncwl-workflow-debug-report.md
Raw artifact contract 
{
  "id": "cwl-workflow-debug-report",
  "kind": "markdown",
  "default_filename": "cwl-workflow-debug-report.md",
  "description": "CWL failure-surface classification with captured run/job/output evidence and a recommended next step or reference-gap follow-up."
}

Consumes

workflow-test-result

Structured run handoff from [[run-workflow-test]]: test result, run/job/artifact context, and the observed CWL failure modality.

Raw artifact contract 
{
  "id": "workflow-test-result",
  "description": "Structured run handoff from [[run-workflow-test]]: test result, run/job/artifact context, and the observed CWL failure modality.",
  "producers": [
    "run-workflow-test"
  ]
}

SKILL.md


# debug-cwl-workflow-output

Follow the procedure below and use the artifact/reference sections as the runtime contract.

## When To Use

- Triage failing CWL run outputs; classify failure modes; propose fixes.

## Inputs

- Read artifact `workflow-test-result`. Produced by `run-workflow-test`. Structured run handoff from run-workflow-test: test result, run/job/artifact context, and the observed CWL failure modality.

## Outputs

- Write artifact `cwl-workflow-debug-report` as `cwl-workflow-debug-report.md`. Format: `markdown`. CWL failure-surface classification with captured run/job/output evidence and a recommended next step or reference-gap follow-up.

## Required Tools

- None declared. Procedure should not assume external CLIs are present.

## Load Upfront

- None declared.

## Load On Demand

- None declared.

## Validation

- None declared.

## Procedure

Triage a failing CWL run: classify the failure mode from logs and outputs and propose a fix routed to the authoring step responsible for it.

## Runtime Notes

- Do not read Foundry source files at runtime; use only files packaged in this skill bundle and user-supplied artifacts.
- Preserve declared artifact filenames unless the user or harness supplies explicit paths.
- Carry unresolved assumptions into the output artifact instead of silently inventing missing source evidence.