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Prevent adapter trimming with porechop on PacBio reads #1012

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Merged
dialvarezs merged 2 commits into from
Apr 5, 2026
+15 −4
Merged

Prevent adapter trimming with porechop on PacBio reads #1012

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27c7ec9
fix: prevent adapter trimming with porechop on pb reads
dialvarezs Apr 5, 2026
be7e98b
chore: update changelog
dialvarezs Apr 5, 2026
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#1012](https://github.com/nf-core/mag/pull/1012) - Prevent adapter trimming with Porechop on PacBio reads (by @dialvarezs)

### `Dependencies`

### `Deprecated`
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17 changes: 13 additions & 4 deletions subworkflows/local/preprocessing_longread/main.nf
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Expand Up @@ -34,21 +34,30 @@ workflow LONGREAD_PREPROCESSING {

if (!params.assembly_input) {
if (!params.skip_adapter_trimming && !val_skip_qc) {
ch_long_reads_by_platform = ch_raw_long_reads.branch { meta, _reads ->
ont: meta.lr_platform in ['OXFORD_NANOPORE', 'OXFORD_NANOPORE_HQ']
pb: meta.lr_platform in ['PACBIO_CLR', 'PACBIO_HIFI']
}
ch_long_reads = channel.empty()

// PacBio reads bypass adapter trimming for now, as there is no tool for that.
ch_long_reads = ch_long_reads.mix(ch_long_reads_by_platform.pb)

if (params.longread_adaptertrimming_tool && params.longread_adaptertrimming_tool == 'porechop_abi') {
PORECHOP_ABI(
ch_raw_long_reads,
ch_long_reads_by_platform.ont,
[],
)
ch_versions = ch_versions.mix(PORECHOP_ABI.out.versions)
ch_long_reads = PORECHOP_ABI.out.reads
ch_long_reads = ch_long_reads.mix(PORECHOP_ABI.out.reads)
ch_multiqc_files = ch_multiqc_files.mix(PORECHOP_ABI.out.log)
}
else if (params.longread_adaptertrimming_tool == 'porechop') {
PORECHOP_PORECHOP(
ch_raw_long_reads
ch_long_reads_by_platform.ont
)
ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions)
ch_long_reads = PORECHOP_PORECHOP.out.reads
ch_long_reads = ch_long_reads.mix(PORECHOP_PORECHOP.out.reads)
ch_multiqc_files = ch_multiqc_files.mix(PORECHOP_PORECHOP.out.log)
}
}
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