From 8f863575c0db4280ba687b8fbf4e1a5959a5e2df Mon Sep 17 00:00:00 2001 From: Neil Horner Date: Wed, 8 Jul 2026 11:41:37 +0000 Subject: [PATCH] Use -ub for cDNA [CW-7384] --- CHANGELOG.md | 5 +++++ main.nf | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e7aca5b..aa6090b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [Unreleased] + +### Fixed +- Incorrect strand assignment when mapping cDNA reads is fixed by using minimap2 `-ub` instead of `-uf`. + ## [v2.0.1] This patch release of `wf-transcriptomes` handles an additional quantification failure edge case that was not observed before release, fixes issues encountered by users during joint discovery when providing many samples, and makes some improvements to the volcano plot in the output report. diff --git a/main.nf b/main.nf index 6d8c966..0ba8d9d 100644 --- a/main.nf +++ b/main.nf @@ -256,7 +256,7 @@ workflow { def ingress_args = [ "minimap2_memory": ["31GB", "62GB"], - "minimap2_opts": params.direct_rna ? "-ax splice -uf -k14" : "-ax splice -uf", + "minimap2_opts": params.direct_rna ? "-ax splice -uf -k14" : "-ax splice -ub", "alignment_threads": 12, "output_xam_fmt": "bam", "sample": params.sample,