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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. freeform-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

Run this pipeline

/ stop-gap harness

Run this pipeline today via its assembled harness skill pipeline-paper-to-cwl — install once (setup), then in a Claude Code session: 

/foundry-skills:pipeline-paper-to-cwl

Each run gets its own ./<run-slug>/ working directory so artifacts stay namespaced and a second run won't clobber the first — the harness sets this up first (phase detail).

phases
11
auto casts
1
manual
10
loops
3

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.

summarize-paper now emits the shared freeform-summary handoff, so the design phase is shared with future interview-sourced CWL starts.