CWL Conditional Workflow Support in Galaxy

CWL v1.2 Conditional Features

CWL v1.2 introduced three key conditional features:

1. when — Step-level boolean expression; if false, step is skipped and outputs are null
2. pickValue — Workflow output/step input directive for merging multiple sources:
   • first_non_null — return first non-null from source list
   • the_only_non_null — validate exactly one non-null, return it
   • all_non_null — return array of all non-null values
3. MultipleInputFeatureRequirement — Required when outputSource or step input source is a list

What’s Implemented

Multiple input connections — WORKING

Galaxy already supports multiple connections to step inputs. 7 non-conditional multiple_input tests pass across v1.1/v1.2 (e.g. wf_multiplesources_multipletypes, wf_wc_scatter_multiple_merge, valuefrom_wf_step_multiple). The plumbing:

• input_connections_by_step() at parser.py:668 calls split_step_references() with default multiple=True, building lists of connections per input name
• linkMerge is parsed at parser.py:1028-1029 and stored as merge_type
• MultipleInputFeatureRequirement listed in SUPPORTED_TOOL_REQUIREMENTS (not enforced, but not rejected)

This confirms Galaxy’s workflow model handles multi-source connections — the gap is specifically in how workflow outputs (not inputs) reference multiple sources.

when expressions — WORKING

Galaxy has full support for step-level when expressions:

Parsing (CWL→Galaxy workflow):

• parser.py:1115 — ToolStepProxy.to_dict() extracts when from CWL step

Runtime evaluation:

• modules.py:474-526 — evaluate_value_from_expressions() evaluates when via do_eval() (CWL JS engine)
• modules.py:1137-1161 — Subworkflow module propagates when_values through slice_collections()
• modules.py:2765-2771 — CWL tool module evaluates when per scatter slice
• run.py:403-418 — WorkflowProgress tracks when_values list
• modules.py:3024 — Steps with when_values == [False] have outputs hidden

Bug: SubworkflowStepProxy.to_dict() at parser.py:1137-1154 does NOT extract the when expression (only ToolStepProxy does). Conditional subworkflow steps lose their when condition during import.

What’s NOT Implemented

Multiple outputSource — NOT SUPPORTED

The crash point for all_non_null_all_null and all pickValue tests:

parser.py:607  get_outputs_for_label()
  → calls split_step_references(output["outputSource"], multiple=False, ...)
parser.py:982  split_step_references()
  → assert len(split_references) == 1  ← CRASH

get_outputs_for_label() hardcodes multiple=False, but the list outputSource pattern (e.g. outputSource: [step1/out1, step2/out1]) is exclusively a CWL v1.2 conditional feature — no non-conditional tests exercise this path. All the existing multiple_input tests that pass use multiple sources on step inputs, not workflow outputs.

pickValue — NOT IMPLEMENTED

No parsing, serialization, or runtime logic for pickValue exists anywhere in Galaxy source.

Test Status (v1.2 conditional tests)

GREEN (passing) — 13 tests

Simple when + single outputSource (no pickValue needed):

• direct_optional_null_result / _nojs / direct_required / _nojs — single step, when=false, output=null
• direct_optional_nonnull_result / _nojs — single step, when=true
• condifional_scatter_on_nonscattered_true — scatter with single source

should_fail validation tests (pass because workflow import crashes on multiple outputSource):

• first_non_null_all_null / _nojs — all sources null with first_non_null
• pass_through_required_fail / _nojs — multiple non-null with the_only_non_null
• all_non_null_multi_with_non_array_output / _nojs — all_non_null on non-array type
• the_only_non_null_multi_true / _nojs — multiple non-null with the_only_non_null
• conditionals_non_boolean_fail / _nojs — non-boolean when result

RED (failing) — 27 tests

All tests requiring pickValue or multiple outputSource at the workflow output level:

pickValue: first_non_null (crash on multiple outputSource):

• pass_through_required_false_when / _nojs / _true_when / _nojs
• first_non_null_first_non_null / _nojs / _second_non_null / _nojs

pickValue: the_only_non_null (crash on multiple outputSource):

• pass_through_required_the_only_non_null / _nojs
• the_only_non_null_single_true / _nojs

pickValue: all_non_null (crash on multiple outputSource):

• all_non_null_all_null / _nojs / _one_non_null / _nojs / _multi_non_null / _nojs

Scatter + conditional (various failures):

• condifional_scatter_on_nonscattered_false / _nojs
• scatter_on_scattered_conditional / _nojs
• conditionals_nested_cross_scatter / _nojs
• conditionals_multi_scatter / _nojs

Complex conditional + defaults:

• cond-with-defaults-1 / cond-with-defaults-2

Architecture Gaps

To implement pickValue, Galaxy would need:

1. Parser changes (parser.py):

   • get_outputs_for_label() must handle list outputSource (pass multiple=True)
   • Store pickValue directive on workflow output metadata
   • Multiple input connections already work, so the underlying model supports this

2. Runtime changes (modules.py / run.py):

   • Apply pickValue semantics when collecting workflow outputs
   • Handle null-filtering (first_non_null, all_non_null) and validation (the_only_non_null)

3. Scatter + conditional combination:

   • Some scatter tests produce null elements that need filtering
   • condifional_scatter_on_nonscattered_false expects out1: [] — all scatter elements skipped

Unresolved Questions

• Should pickValue be a Galaxy-level workflow feature or only CWL?
• How should null outputs from skipped steps interact with Galaxy’s collection model?