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Prevent running ALE on long read data #1017

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Merged
dialvarezs merged 2 commits into from
Apr 9, 2026
+2 −5
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Prevent running ALE on long read data #1017

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dcdb6d9
fix: prevent running ALE on long read data
dialvarezs Apr 9, 2026
c913623
chore: update changelog
dialvarezs Apr 9, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#1012](https://github.com/nf-core/mag/pull/1012) - Prevent adapter trimming with Porechop on PacBio reads (by @dialvarezs)
- [#1011](https://github.com/nf-core/mag/pull/1011) - Fix issue making CheckM2 running only for one sample per run (by @dialvarezs)
- [#1017](https://github.com/nf-core/mag/pull/1017) - Prevent ALE running on long read assemblies when a sample has both LR and SR data (reported by @jfy133, fix by @dialvarezs)

### `Dependencies`

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6 changes: 1 addition & 5 deletions workflows/mag.nf
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Expand Up @@ -275,12 +275,8 @@ workflow MAG {
*/

if (!params.skip_ale) {
ch_shortread_assemblies_for_ale = ch_assemblies.filter { meta, _assembly ->
meta.sr_platform != null && meta.sr_platform != []
}

ch_ale_input = BINNING_PREPARATION.out.grouped_mappings
.join(ch_shortread_assemblies_for_ale, by: 0)
.join(ch_shortread_assemblies, by: 0)
.map { meta, _contigs, bams, _bais, assembly ->
// Try to find the BAM where reads came from the same sample as the assembly (co-binning may include multiple BAMs)
// If none matches (coassembly), take the first one after sorting for determinism
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