CWL when:/pickValue → Galaxy branching translation

Audience: a Mold author looking at a summary-cwl.json whose steps carry when: predicates and/or whose workflow outputs use pickValue, deciding which Galaxy translation to recommend.

The three honest translations

CWL has two related branching mechanisms with no 1:1 gxformat2 equivalent (until galaxy#22222 — see cwl-pickvalue-to-galaxy):

• when: on a step — execute conditionally on a JS predicate.
• pickValue: on a step input or workflow output — fan in N candidate sources and pick first_non_null / the_only_non_null / all_non_null.

Three Galaxy-idiomatic translations are available; each is honest for a different source shape.

Translation A — paired_or_unpaired collection (preferred when the discriminator is paired-vs-single)

When the CWL when: predicates discriminate the paired-vs-single mode of read inputs (the seqprep-subwf pattern: single_reads: File? triggers single mode; absence triggers paired mode), the entire branching collapses into a single workflow with a paired_or_unpaired (or list:paired_or_unpaired for batches) input.

• The mode-switch parameter disappears.
• The per-step when: predicates disappear.
• The pickValue fan-in disappears — both branches feed the same wrapper, branching happens inside the wrapper via has_single_item.
• Result: one workflow, fewer steps, no synthetic merge.

See [[galaxy-paired-or-unpaired-collections]] for the type itself and the decision rule.

Translation B — native pick_value workflow step (preferred for non-collection-shaped branches, post galaxy#22222)

When the CWL pickValue is on the workflow output (or a step input) but the discriminator is not a collection-shape concern (e.g., it’s a parameter-driven mode, or branches that produce different artifact kinds, or all_non_null aggregation), use Galaxy’s native pick_value workflow module.

• Each upstream branch keeps a per-step gxformat2 when: predicate.
• A type: pick_value step with state.mode: <cwl_mode> fans in the branch outputs.
• Workflow output reads from the pick_value step’s output.

See [[cwl-pickvalue-to-galaxy]] for the full mapping (mode table, gxformat2 surface, gotchas, version floor).

Translation C — sibling workflows per mode (preferred when IWC convention exists or modes diverge structurally)

When the IWC corpus already publishes the same upstream pipeline as two separate workflow files (one per mode), follow the IWC convention. Same applies when the two CWL branches diverge structurally beyond a single fan-in point (different downstream steps per mode, not just different sources to the same output).

• Each Galaxy .gxwf.yml is a linear workflow with no branching.
• Two sibling files: <name>-paired.gxwf.yml, <name>-single.gxwf.yml.
• Downstream consumers (and registries) pick the workflow that matches their data shape.

Evidence: EBI-Metagenomics/pipeline-v5 → IWC ports amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-quality-control-paired-end and …-single-end.

Picking among A / B / C

Decision walk for the data-flow Mold:

1. Is the discriminator paired-vs-single reads (or a near-cousin: optional File? read inputs gated by when:)? → A. Translation B/C are fallbacks if paired_or_unpaired cannot model the shape (e.g., scatter/nesting depth limit; see [[galaxy-paired-or-unpaired-collections]] §“Limitation: only deepest rank”).
2. Does an IWC port of the same upstream pipeline exist as sibling workflows? → C, unless updating to paired_or_unpaired (A) is explicitly an upgrade. Surface both options in compare-against-iwc-exemplar’s comparison notes.
3. Does the workflow output use pickValue: all_non_null (collection aggregation), or does the branching produce structurally divergent outputs that need first-non-null/the-only-non-null fan-in? → B.
4. None of the above (custom predicate, non-paired-mode when:) → B (default to native pick_value). Use C only if the branches share no downstream structure.

Anti-patterns to call out in the brief

• Synthesizing a “pick non-empty” custom Galaxy tool. With galaxy#22222 (pick_value module), this is no longer needed and is now an anti-pattern. The Foundry’s prior data-flow briefs that recommended this should be updated.
• Emitting a workflow-level reads_mode select parameter when the discriminator is collection-shape. Use translation A instead.
• Translating CWL first_non_null to Galaxy first_or_skip without flagging that this is a Galaxy-only semantic (first_or_skip emits a “skipped” HDA on all-null; CWL first_non_null errors). Don’t swap modes silently.

Source-side anti-patterns to surface

CWL sources sometimes carry mode-switch branching that is a CWL accommodation rather than a real design choice. Surface these as anti-pattern flags during the data-flow brief:

• Bespoke per-pipeline utility scripts (count_lines.py, ad-hoc renamers) that emit scalar metrics consumable only via CWL’s typed workflow outputs. Galaxy convention: drop them in favor of MultiQC / fastp JSON / FastQC reports.
• Decompress-just-to-pass-through chains (CWL multiple-gunzip.cwl step that exists because the next CWL tool refuses gzipped input). Galaxy tools commonly accept .fastq.gz directly; verify before keeping the unzip step. Where IWC keeps it (e.g., __UNZIP_COLLECTION__ in MGnify amplicon ports), the downstream is intentional.

Galaxy version floor

Translation B (native pick_value) requires Galaxy ≥ main 2026-03-31 (galaxy#22222 merge date). Workflows using type: pick_value will not import on older releases. Translations A and C have no recent version floor (A requires paired_or_unpaired support, present since PR #19377 / late 2024).

Citations

• [[cwl-pickvalue-to-galaxy]] — full PR analysis of galaxy#22222 (the native pick_value module).
• [[galaxy-paired-or-unpaired-collections]] — the discriminated-union collection type and the paired ⊏ paired_or_unpaired subtyping lattice.
• IWC sibling-workflows convention: amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-quality-control-paired-end and …-single-end in the IWC corpus.
• Run-dir evidence for the discriminator-classification trap: casts/claude/skills/_emulated-runs/mgnify-seqprep-subwf/cwl-galaxy-interface.md (the under-read Option A) vs the now-recommended translation A.

Evidence quality

• Corpus-observed (concrete): IWC sibling-workflows precedent for the paired-vs-single MGnify pipeline.
• Galaxy-source-observed (concrete via referenced notes): pick_value semantics, paired_or_unpaired subtyping.
• Foundry-inference (marked): the three-translation taxonomy and the decision walk are inferred from one run + IWC evidence; refine after more CWL→Galaxy test-drives.
• Anti-pattern catalog: corpus-grounded for count_lines.py (one run) and unzip-just-to-pass-through (same run); expect drift as more CWL fixtures land.