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PAPER → CWL

Direct path from a paper to a CWL Workflow + CommandLineTool set.

draft pipelinesource/papertarget/cwl

Phases

/ subway map 11 phases
  1. summarize-paper
  2. paper-summary-to-cwl-design
  3. summary-to-cwl-template
  4. summarize-cwl-tool loop
  5. implement-cwl-tool-step loop
  6. validate-cwl loop
  7. branch test-data-resolution
    1. paper-to-test-data
    2. find-test-data
    3. user-supplied
  8. implement-cwl-workflow-test
  9. validate-cwl
  10. run-workflow-test
  11. debug-cwl-workflow-output

PAPER → CWL

Direct path. Lifted from docs/HARNESS_PIPELINES.md §“PAPER → CWL”.

CWL targeting has no discover-or-author branch — wrappers aren’t a separate concern; CommandLineTool authoring is built into the per-step Mold (implement-cwl-tool-step) and is informed by summarize-cwl-tool.