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Fix order-dependent combine(by:) silently dropping samples in QUANT #460

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Fix order-dependent combine(by:) silently dropping samples in QUANT #460

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d69fe1e
Fix order-dependent combine(by:) in QUANT by unwrapping groupKey to i…
jonasscheid Jun 3, 2026
4abe5c4
Add CHANGELOG entry for QUANT combine fix (#460)
jonasscheid Jun 3, 2026
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Updated to nf-core template 4.0.2 [#454](https://github.com/nf-core/mhcquant/pull/454)
- Updated all nf-core modules to their latest versions [#454](https://github.com/nf-core/mhcquant/pull/454)

### `Fixed`

- Fixed silent per-sample drop from order-dependent `combine(by:)` in QUANT [#460](https://github.com/nf-core/mhcquant/pull/460)

### `Dependencies`

| Dependency | Old version | New version |
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7 changes: 6 additions & 1 deletion subworkflows/local/quant/main.nf
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Expand Up @@ -44,8 +44,13 @@ workflow QUANT {

// Manipulate such that [meta_run1, idxml_run1, pout_group1], [meta_run2, idxml_run2, pout_group1] ...
ch_runs_score_switched
// Nextflow can only combine/join on the exact groupKey object, merge_id is not sufficient
.map { meta, idxml -> [groupKey([id: "${meta.sample}_${meta.condition}"], meta.group_count) , meta, idxml] }
// Combine on the unwrapped key.target ([id] map), NOT the groupKey object: GroupKey.equals()
// is asymmetric (groupKey.equals(map)==true but map.equals(groupKey)==false), so a
// groupKey-vs-map combine silently drops pairs depending on operand arrival order on AWS Batch
// (nextflow-io/nextflow#4104). filter_q_value carries the same [id] map, so map-vs-map equals
// is symmetric and order-independent.
.map { key, meta, idxml -> [key.target, meta, idxml] }
.combine(filter_q_value, by:0)
.map { group_meta, meta, idxml, q_value -> [meta, idxml, q_value] }
.set { ch_runs_to_filter}
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