From 27c7ec95a08a6b1376afa1bac969f00a334f6fcf Mon Sep 17 00:00:00 2001 From: "Diego Alvarez S." Date: Sun, 5 Apr 2026 10:51:25 -0400 Subject: [PATCH 1/2] fix: prevent adapter trimming with porechop on pb reads --- .../local/preprocessing_longread/main.nf | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/preprocessing_longread/main.nf b/subworkflows/local/preprocessing_longread/main.nf index 5094bd736..9995fea36 100644 --- a/subworkflows/local/preprocessing_longread/main.nf +++ b/subworkflows/local/preprocessing_longread/main.nf @@ -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) } } From be7e98b5747b42f88ce884419548a66bbb3f1f7d Mon Sep 17 00:00:00 2001 From: "Diego Alvarez S." Date: Sun, 5 Apr 2026 10:53:26 -0400 Subject: [PATCH 2/2] chore: update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 769354926..f90be1140 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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`