CWL pickValue → Galaxy pick_value

Audience: a Mold author who just saw a pickValue:* marker in a summary-cwl.json edge via: array (or a WorkflowOutputParameter.output_source multi-value carrying a pickValue hint) and needs to emit gxformat2.

CWL pickValue — canonical semantics

Source: CWL v1.2 schema Workflow.yml (PickValueMethod) and the rendered spec at https://www.commonwl.org/v1.2/Workflow.html#PickValueMethod.

• first_non_null — “For the first level of a list input, pick the first non-null element. The result is a scalar. It is an error if there is no non-null element.”
• the_only_non_null — “For the first level of a list input, pick the single non-null element. The result is a scalar. It is an error if there is more than one non-null element.”
• all_non_null — “For the first level of a list input, pick all non-null values. The result is a list, which may be empty.”

Placement: declared on both WorkflowStepInput and WorkflowOutputParameter with identical semantics. Operates on the array produced when source: / outputSource: is multi-valued. First level only; composes with linkMerge (which builds the array pickValue then filters).

Interaction with when: — pickValue is the canonical fan-in idiom for N branches gated by complementary when: predicates. Skipped steps emit null for their outputs; the survivor is picked. (Inference, but corroborated by the PR’s stated motivation: unblocking 27+ CWL v1.2 conditional conformance tests.)

Galaxy pick_value — what galaxy#22222 added

PR https://github.com/galaxyproject/galaxy/pull/22222 (merged 2026-03-31, author jmchilton, labels area/workflows, area/cwl).

• New workflow module type: pick_value. Registered at lib/galaxy/workflow/modules.py module_types["pick_value"] = PickValueModule (~line 3108 at PR head). No DB migration — reuses WorkflowStep.type = "pick_value" + tool_state = {"mode": "...", "num_inputs": N} + standard WorkflowStepConnection / WorkflowOutput.

• Four modes (Galaxy is a superset of CWL by one extra mode):

  Galaxy mode	Maps to CWL	All-null behavior	Output shape
  first_non_null	first_non_null	Fail workflow (FailWorkflowEvaluation)	scalar dataset
  first_or_skip	(no CWL equivalent)	Emit a “skipped” HDA (extension=expression.json, blurb=skipped)	scalar (or skipped)
  the_only_non_null	the_only_non_null	Fail; also fails when >1 non-null	scalar dataset
  all_non_null	all_non_null	Returns an HDCA list (may be empty)	list collection

• Null detection is two-pronged (PickValueModule._pick_from_replacements, ~modules.py:2060–2068):

  • the NO_REPLACEMENT sentinel (no upstream connection, or upstream step was skipped via when:); or
  • an HDA with extension == "expression.json" and blurb == "skipped".

• gxformat2 surface (from PR test fixtures, e.g. lib/galaxy_test/workflow/pick_value_first_non_null_mapped.gxwf.yml):

  pick:
    type: pick_value
    in:
      input_0:
        source: branch_a/out_file1
      input_1:
        source: branch_b/out_file1
    state:
      mode: first_non_null

  Inputs are named input_0 … input_{N-1}. The single output is named output. The editor exposes one extra empty terminal for grow-on-connect (PR body §“get_all_inputs()”).

• Mapping over collections is supported (_execute_mapped, modules.py ~2130). When inputs are collections, the module iterates per-element. Output shape: list for the scalar modes, list:list for all_non_null (modules.py ~2211–2215).

• CWL importer not yet wired. The PR body explicitly says “Once CWL import integration is added, it will unblock 27+ CWL v1.2 conditional conformance tests.” The runtime is in main as of 2026-03-31; the importer mapping pickValue → pick_value is future work. Translator Molds cannot yet punt to Galaxy’s CWL importer — the gxformat2 file we emit must already contain the pick_value step.

Mapping table

Cases that don’t translate cleanly:

• scatter + pickValue on the same step input. Galaxy supports per-element mapping, but the composition is unusual in CWL; verify per-fixture (inference).
• Deeply nested linkMerge: merge_nested (>1 level). Galaxy pick_value operates at first level only (inference from MODES + execute logic); deeply nested cases may need a translator flag.

Translation guidance for cwl-summary-to-galaxy-data-flow

Given a summary-cwl.json whose graph.edges[].via contains "pickValue:<mode>" (or whose workflow_outputs[].output_source is multi-valued — when the typed-pick_value field is added to the schema, prefer that):

1. Detect by edge fan-in pattern. Group edges by to (workflow-output id or step-input id) where via contains a pickValue:* token. Each group becomes one pick_value step.
2. Emit a pick_value step per group. Suggested step id pick_<output_id>. Inputs input_0, input_1, … in CWL declaration order. state.mode is the CWL mode verbatim.
3. Rewire the workflow output to read from the new pick step’s output rather than the multi-source outputSource array.
4. When pickValue is on a step input, insert the pick_value step upstream of that step and rewire its input to a single source.
5. Preserve upstream when: predicates unchanged. pick_value consumes whatever each branch emits (real dataset or skipped HDA) and decides at execution.
6. Type-shape warning for all_non_null: the workflow output type changes from a CWL scalar T (post-pickValue) to a Galaxy list HDCA. Surface in the brief.
7. Do not invent a “pick non-empty” custom tool. Use the native pick_value module — prior Foundry recommendations to synthesize a picker step are superseded.
8. Two-sibling-workflow fallback stays valid for readability when the entire DAG splits cleanly on a single mode predicate (IWC convention: see EBI-Metagenomics/pipeline-v5 ↔ amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-quality-control-paired-end / …-single-end). With #22222 merged, the single-workflow pick_value translation is now also viable; the template Mold may choose either.

Risks, gotchas, open issues

• Importer not wired (PR-observed). Translators must emit the pick_value step themselves; Galaxy’s CWL importer won’t convert pickValue automatically yet.
• No CWL-direct mode for first_or_skip. Translator should never silently emit it from CWL input — only when the human author asks for skip-propagation semantics.
• the_only_non_null is strict. Fails on >1 non-null too. Don’t swap modes during translation.
• Empty all_non_null result is legal. Downstream tools must accept empty collections.
• pick_value is a step, not a step-input attribute. Translator can’t represent a CWL inline pickValue on a step input without adding a real Galaxy step — step count increases vs CWL.
• Mapped-collection output shape. all_non_null over mapped inputs yields list:list. Consumers expecting flat list will break.
• Galaxy version floor. This module landed on main 2026-03-31. Workflows using type: pick_value will not import on older Galaxy releases. Translator should emit a metadata note / required-version hint when the draft uses pick_value.
• summary-cwl schema gap. The Foundry’s summary-cwl.json schema currently encodes workflow-level pickValue only via edge via markers; first-class pick_value on WorkflowOutput would make detection trivial. Open work tracked in content/molds/summarize-cwl/refinements/2026-05-11-mgnify-seqprep-subwf.md.

Citations

• PR metadata + body: https://github.com/galaxyproject/galaxy/pull/22222.
• PickValueModule implementation: lib/galaxy/workflow/modules.py lines 1951–2128 at PR head (mode list, error semantics, null detection, mapped execution).
• gxformat2 surface examples: lib/galaxy_test/workflow/pick_value_first_non_null_mapped.gxwf.yml, pick_value_all_non_null_mapped.gxwf.yml, pick_value_skip_pja.gxwf.yml at PR head.
• CWL spec: PickValueMethod doc strings in https://raw.githubusercontent.com/common-workflow-language/cwl-v1.2/main/Workflow.yml; rendered at https://www.commonwl.org/v1.2/Workflow.html#PickValueMethod.
• IWC fallback exemplar: amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-quality-control-paired-end / …-single-end (sibling-workflows convention).

Evidence quality

• PR-observed (concrete): module type, modes, gxformat2 surface, mapped-collection output shape, importer not yet wired, version floor.
• CWL-spec (concrete): mode definitions and error conditions; placement on WorkflowStepInput and WorkflowOutputParameter.
• Inference (marked inline): pickValue composing with when:; step-input-side translation requiring an upstream step; scatter + pickValue rarity; deeply-nested linkMerge interaction.