Missing CWL Workflow Mapping/Scatter Features in Galaxy

Summary of failing CWL conformance tests related to scatter, cross product, merge, and multi-input mapping features that Galaxy has not yet implemented.

Overview

Galaxy currently supports only dotproduct scatter for multi-input cases. The flat_crossproduct and nested_crossproduct scatter methods are explicitly unimplemented. Merge operations are partially implemented. Scatter + conditional combinations also fail. All tests below are marked RED (known failing).

Two Distinct Scatter Code Paths

Galaxy has two separate code paths for scatter execution, which produce different failure modes:

1. CWL tool steps use find_cwl_scatter_collections() (modules.py:412-481). This function has no assertion on scatter type — it silently treats all scatter methods as dotproduct, producing wrong results (CompareFail).

2. Subworkflow steps use _find_collections_to_match() via compute_collection_info() (modules.py:818→843). This path has a hard assertion that blocks flat/nested crossproduct:

   assert scatter_type in ["dotproduct", "disabled"], f"Unimplemented scatter type [{scatter_type}]"

   This produces Final state - failed (assertion propagates as unexpected failure).

The v1.0/v1.1 crossproduct tests scatter on CommandLineTool steps (path 1), while the v1.2 nested-scatter tests scatter on subworkflow steps (path 2).

Feature Gap 1: flat_crossproduct Scatter Method (NOT IMPLEMENTED)

CWL spec: Given scatter: [A, B] with scatterMethod: flat_crossproduct, the runner should create N×M jobs (cartesian product) and return a flat array of results.

Failing Tests

Impact

• 3 tests fail across all three CWL versions (v1.0, v1.1, v1.2)
• 3 additional tests fail in v1.2 only (subworkflow scatter combinations)

Feature Gap 2: nested_crossproduct Scatter Method (NOT IMPLEMENTED)

CWL spec: Given scatter: [A, B] with scatterMethod: nested_crossproduct, the runner should create N×M jobs and return a nested array-of-arrays structure.

Same two failure modes as flat_crossproduct: silent dotproduct fallback for tool steps, assertion error for subworkflow steps.

Failing Tests

Impact

• 4 tests fail across all three CWL versions
• 3 additional tests fail in v1.2 only

Feature Gap 3: dotproduct + valueFrom (BROKEN)

Dotproduct scatter combined with valueFrom expressions on step inputs fails.

Failing Tests

Note: valuefrom_wf_step (also in RED_TESTS for all versions) is NOT scatter-related — it tests valueFrom on a non-scattered step input and fails for different reasons.

Feature Gap 4: Scatter into Subworkflows (BROKEN)

Scatter into subworkflow steps fails even with basic dotproduct scatter. Galaxy’s SubWorkflowModule passes the entire HDCA collection reference to the subworkflow instead of scattering individual elements.

Failing Tests

Root Cause

SubWorkflowModule._find_collections_to_match() via compute_collection_info() doesn’t properly decompose collections for scatter into subworkflow steps. The assertion at modules.py:843 also blocks non-dotproduct methods entirely.

Feature Gap 5: Scatter + Conditional (when) Interactions (BROKEN)

Plan: Folded into CWL_CONDITIONALS_PICK_VALUE_FRAMEWORK_SUPPORT.md (pickValue plan covers all 9 tests). The int[] defaults fix is Phase 0; scatter null filtering is Pattern B (Phase 6). conditionals_nested_cross_scatter also requires GAP2.

CWL v1.2 added when clauses to workflow steps. When combined with scatter, the spec says null results from skipped (condition=false) scatter elements should be removed from the output array. Galaxy retains nulls or fails entirely.

Failing Tests — JavaScript Variants

Failing Tests — No-JavaScript Variants

These use pickValue instead of JS when expressions. They fail at invocation time with HTTP 400 because Galaxy treats the workflow inputs as non-optional:

Note: “condifional” (sic) is the actual test ID spelling in the CWL conformance suite.

Root Causes

1. Galaxy doesn’t filter null values from scatter output when when condition skips elements
2. No-JS conditional workflows fail because Galaxy doesn’t recognize conditional inputs as optional
3. nested_crossproduct + conditionals combines two unimplemented features

Feature Gap 6: merge_nested for Non-Collection Inputs (PARTIAL)

CWL’s linkMerge: merge_nested wraps multiple step inputs into a nested list. Galaxy implements this for list→list:list promotion but raises NotImplementedError when merging individual datasets.

Evidence — lib/galaxy/workflow/run.py:515-517:

if input_collection_type is None:
    if merge_type == "merge_nested":
        raise NotImplementedError()

Note: merge_flattened has a similar gap — run.py:550-551 raises NotImplementedError for non-list collection types, though no current RED_TESTS exercise this path.

Failing Tests

Complete Test List (30 unique scatter/map/reduce failures)

Cross-version failures (appear in v1.0, v1.1, and v1.2):

1. wf_scatter_two_flat_crossproduct
2. wf_scatter_flat_crossproduct_oneempty
3. wf_scatter_twoparam_flat_crossproduct_valuefrom
4. wf_scatter_two_nested_crossproduct
5. wf_scatter_nested_crossproduct_firstempty
6. wf_scatter_nested_crossproduct_secondempty
7. wf_scatter_twoparam_nested_crossproduct_valuefrom
8. wf_scatter_twoparam_dotproduct_valuefrom

v1.1 + v1.2 failures:

9. scatter_embedded_subworkflow
10. scatter_multi_input_embedded_subworkflow

v1.2-only failures:

11. condifional_scatter_on_nonscattered_false (sic)
12. condifional_scatter_on_nonscattered_false_nojs (sic)
13. condifional_scatter_on_nonscattered_true_nojs (sic)
14. conditionals_multi_scatter
15. conditionals_multi_scatter_nojs
16. conditionals_nested_cross_scatter
17. conditionals_nested_cross_scatter_nojs
18. dotproduct_dotproduct_scatter
19. dotproduct_simple_scatter
20. flat_crossproduct_flat_crossproduct_scatter
21. flat_crossproduct_simple_scatter
22. nested_crossproduct_nested_crossproduct_scatter
23. nested_crossproduct_simple_scatter
24. scatter_on_scattered_conditional
25. scatter_on_scattered_conditional_nojs
26. simple_dotproduct_scatter
27. simple_flat_crossproduct_scatter
28. simple_nested_crossproduct_scatter
29. simple_simple_scatter
30. wf_wc_nomultiple_merge_nested

Note: tests 1-8 are the same logical tests re-run against each CWL spec version (the conformance suite reuses test IDs across v1.0/v1.1/v1.2). They also appear in the v1.2 RED_TESTS list.

Key Source Files

Summary of Implementation Gaps