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fix: sort BAM/BAI inputs to Manta for deterministic sample order #815

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ramprasadn merged 2 commits into from
Apr 22, 2026
Merged

fix: sort BAM/BAI inputs to Manta for deterministic sample order #815

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490b687
fix: sort BAM/BAI inputs to Manta for deterministic sample order
Apr 18, 2026
974a32a
Merge branch 'dev' into fix/manta-sample-sort
ramprasadn Apr 21, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -59,6 +59,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- Ensure deterministic sample ordering in Manta SV output by sorting BAM/BAI channel inputs [#815](https://github.com/nf-core/raredisease/pull/815)
- Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714)
- Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733)
- Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745)
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6 changes: 4 additions & 2 deletions subworkflows/local/call_sv_manta/main.nf
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Expand Up @@ -16,11 +16,13 @@ workflow CALL_SV_MANTA {
val_analysis_type // string: "wes", "wgs", or "mito"

main:
ch_bam.collect{_meta, bam -> bam}
ch_bam.map{ _meta, bam -> bam }
.collect(sort: { a, b -> a.getName() <=> b.getName() })
.toList()
Comment on lines +19 to 21

@fellen31 fellen31 Apr 20, 2026

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Nice! Good that you found this issue. Previously I've sorted the inputs within the module for these kinds of issues (e.g. https://github.com/nf-core/modules/blob/5d4a8ab3aeed5b759ca0a38b57b6153e9b55deab/modules/nf-core/bcftools/merge/main.nf#L26). But maybe this works since it's converted to a list before it's combined into manta_input? @ramprasadn, what's the reason for having .toList() here in the first place?

@ramprasadn ramprasadn Apr 21, 2026

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Without toList(), the combine operation downstream doesn't work. Instead of [meta, [bam1, bam2], [bai1, bai2]] you get [meta, bam1, bam2, bai1, bai2]

.set { bam_file_list }

ch_bai.collect{_meta, bai -> bai}
ch_bai.map{ _meta, bai -> bai }
.collect(sort: { a, b -> a.getName() <=> b.getName() })
.toList()
.set { bai_file_list }

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