Conditional: gate on non-empty result

Tool

Use a Galaxy when: gate whose boolean input is computed from upstream data shape or content.

The corpus-backed collection recipe is:

collection_element_identifiers -> wc_gnu -> column_maker -> param_value_from_file -> when

MGnify proves this shape in IWC, and the checked verification workflow tests the same operation against Galaxy release_25.1. It is clunky: four shim steps to produce one boolean. Treat it as the known-good recipe until a shorter route validates cleanly.

When to reach for it

Use this when downstream reporting, visualization, or export should run only if an upstream dataset or collection has content.

Common shape:

1. Upstream step may produce an empty result.
2. Workflow computes a boolean from that result.
3. Boolean is connected as an input named when.
4. Downstream reporting/conversion steps declare when: $(inputs.when).

This is not a generic user toggle. If the user chooses whether to run an optional branch, use conditional-run-optional-step.

This is not map-over cleanup. If the need is to drop empty or failed elements inside a collection before the next collection consumer, use collection-cleanup-after-mapover-failure.

This is not __FILTER_NULL__. The conditionals survey found zero __FILTER_NULL__ usage in the IWC corpus, but zero uptake alone is not an anti-pattern call.

Recipe Boundary

This recipe covers data-derived branch admission:

• input fact: “this result is empty/non-empty”;
• output action: “run or skip downstream steps”;
• gate mechanism: boolean-producing shim connected to Galaxy when.

It does not cover routing between mutually exclusive alternatives and merging with pick_value, optional transform then pass-through fallback, filtering collection members, or nullable conditional outputs.

Parameters

Authoring-relevant fields:

• gated step input: id: when, with source from the boolean-producing step or subworkflow output;
• gated step body: when: $(inputs.when);
• collection boolean shim: count identifiers and convert count != 0 to boolean;
• text-like dataset content shim: map empty text to false and non-empty text to true.

Boolean Derivation Mechanics

For collections, the observed IWC recipe is explicit: extract collection element identifiers, count those identifier lines, compute c1 != 0, then read that one-cell result as a boolean parameter.

In MGnify, the embedded subworkflow labeled Map empty/not empty collection to boolean uses collection_element_identifiers, wc_gnu with options: [lines], column_maker with ops.header_lines_select: no and cond: c1 != 0, then param_value_from_file with param_type: boolean and remove_newlines: true.

For text-like datasets, the VGP Hi-C workflow reads the dataset with param_value_from_file as text, then maps "" -> false with map_param_value; unmapped non-empty text defaults to true.

Observed MGnify collection recipe:

collection_element_identifiers
  -> wc_gnu
  -> column_maker with c1 != 0
  -> param_value_from_file
  -> gated Krona / BIOM export steps

This is corpus-backed but intentionally not pretty. Prefer it only when no shorter verified recipe is available.

Idiomatic Shapes

Conceptual gated reporting step:

in:
  - id: input
    source: upstream_result
  - id: when
    source: nonempty_boolean/output_param_boolean
when: $(inputs.when)

Conceptual collection-to-boolean shim:

collection -> collection_element_identifiers -> wc_gnu -> column_maker(c1 != 0) -> param_value_from_file

Conceptual text-like dataset-content shim:

dataset -> param_value_from_file -> map_param_value(empty string = false, non-empty default = true)

These snippets summarize observed and verified shapes. Do not simplify the MGnify chain in a generated workflow until a shorter route validates.

Pitfalls

• Do not lead with the MGnify four-step shim as “best” just because it is corpus-backed. It proves the recipe; it may not be the ideal generated-workflow recipe.
• Do not invent a shorter when expression without validation. Galaxy workflow syntax and tool-form roundtripping need a verified-pattern fixture first.
• Do not use this when the choice is user-controlled. Direct boolean when gates are simpler.
• Do not replace collection cleanup with a workflow gate. Cleanup changes collection members; this pattern skips whole downstream steps.
• Do not cite __FILTER_NULL__ as an IWC-backed conditional pattern. Survey found no corpus uptake.

Verification

The verification test case at verification/workflows/conditional-gate-on-nonempty-result/gate-on-nonempty.gxwf-test.yml passes under Planemo against Galaxy release_25.1 using the MGnify-style shim. The fixture rejected two shorter candidates first: direct when over a collection-derived value failed with when_not_boolean, and an embedded CWL ExpressionTool shim failed gxformat2 validation.

The verified result keeps the MGnify chain as the lead known-good recipe despite the clunkiness.

See Also

• iwc-conditionals-survey — Candidate C decision record and verification outcome.
• iwc-parameter-derivation-survey — parameter-derivation survey that merges non-empty boolean mechanics into this page.
• galaxy-conditionals-patterns — conditionals MOC.
• conditional-run-optional-step — primitive when: branch for user booleans.
• conditional-route-between-alternative-outputs — route alternatives and merge with pick_value.
• collection-cleanup-after-mapover-failure — use when empty/failed collection elements should be dropped or replaced, not when whole downstream steps should be skipped.