gxwf draft-extract

Transform a draft workflow into its already-concretized subset. Pipes three operations from @galaxy-tool-util/schema in order:

1. extractConcreteSubset — drop steps that still carry TODO_* or _plan_*; cascade through dead in: deps; rewrite multi-source inputs to the surviving subset; fall back to default: when a single source dies; recurse into draft subworkflows; drop orphan workflow outputs.
2. stripPlanFields — remove _plan_* planning fields from every surviving step and from the workflow root.
3. promoteFullyConcreteDrafts — flip class: GalaxyWorkflowDraft → class: GalaxyWorkflow on any (sub)workflow now carrying zero TODOs and zero _plan_*. Inner draft with remaining work blocks outer promotion.

Native (.ga) input is rejected — drafts are format2-only. Output format is inferred from the -o extension (.ga / .json → native JSON; otherwise format2 YAML) or, when emitting to stdout, matches the input format. Promoted from the earlier hidden _draft-extract command — same behavior, same flags, now first-class in gxwf --help.

Output

By default, the trimmed workflow is written to stdout. With -o <file>, written to that file. --report-json [file] emits a SingleDraftExtractReport sidecar with dropped_steps, dropped_outputs, rewritten_step_inputs, and the post-extract class.

Examples

gxwf draft-extract workflow.gxwf.yml > concrete.gxwf.yml
gxwf draft-extract workflow.gxwf.yml -o concrete.gxwf.yml --report-json report.json
gxwf draft-extract workflow.gxwf.yml -o concrete.ga
gxwf draft-extract workflow.gxwf.yml | gxwf validate -

Exit codes

• 0 — input parsed and the extract pipeline ran (including the empty-extract case).
• 2 — parse / read failure, native input rejected, or a stdout-sink collision between the workflow output and --report-json=- both targeting stdout.

Gotchas

• This command is a transformation, not a validator. To validate the concrete subset against full gxformat2 rules, pipe to validate (or invoke draft-validate with --concrete, which runs the same pipeline internally).
• The trimmed workflow may still be class: GalaxyWorkflowDraft — promotion only fires when zero TODOs and zero _plan_* remain anywhere (including inside draft subworkflows).
• extractConcreteSubset operates as a fixpoint and is deterministic per-level: drops within a level sort by (round, path); inner-level drops follow their containing surviving subworkflow in source iteration order.
• Outer subworkflow steps are never shrunk in v1 — inner workflows shrink in place. A drafty step at the outer level either survives whole or is dropped whole.
• Use --report-json whenever a cast skill needs to surface which steps were trimmed (e.g., to explain why a downstream test fails on a workflow that “validates fine but is missing the step you asked about”).