# 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 . - **`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 (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`): ```yaml 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 | CWL position | CWL mode | Galaxy translation | | --- | --- | --- | | `WorkflowOutputParameter.outputSource: [a, b, …]` + `pickValue: first_non_null` | `first_non_null` | Insert a `type: pick_value` step with `state.mode: first_non_null`, `input_0: a`, `input_1: b`, …. Wire the pick step's `output` into the workflow `outputs:` block. Direct mapping. | | Same, `the_only_non_null` | `the_only_non_null` | Same shape; `mode: the_only_non_null`. Direct mapping. | | Same, `all_non_null` | `all_non_null` | Same shape; `mode: all_non_null`. **Output type changes**: workflow output becomes a `list` HDCA. Surface to consumers. | | `WorkflowStepInput.source: [a, b]` + `pickValue` | any | Insert a `pick_value` step **upstream** of the consuming step; rewire the step input to consume the pick step's `output`. There is no inline-pick on a step's input in gxformat2 — it must be a real step. (Inference; PR adds a module, not an input-side attribute.) | | `pickValue` over all-null inputs | `first_non_null` / `the_only_non_null` | Galaxy raises `FailWorkflowEvaluation` — matches CWL "It is an error if there is no non-null element". | | Workflow author wants "skipped" rather than "fail" on all-null | *(no CWL mode)* | Use Galaxy-only `first_or_skip`. **Flag in translator that this is a Galaxy extension, not CWL semantics.** Round-tripping back to CWL would require codifying. | 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:"` (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_`. 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: . - `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 ; rendered at . - 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.