From f111755d128ee4c8d77fba5044553fb10eaf165b Mon Sep 17 00:00:00 2001
From: Neil Horner <neil.horner@nanoporetech.com>
Date: Thu, 18 Jan 2024 19:40:14 +0000
Subject: [PATCH] Resolve CW-3327 "Mapping 1 thread"

---
 CHANGELOG.md                       | 4 ++++
 subworkflows/reference_assembly.nf | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fb760b9..bc987a4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 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
+- Mapping stage using a single thread only.
+
 ## [v1.0.0]
 ### Added
 - Published minimap2 and pychopper results to output directory.
diff --git a/subworkflows/reference_assembly.nf b/subworkflows/reference_assembly.nf
index f0bd299..7ab994a 100644
--- a/subworkflows/reference_assembly.nf
+++ b/subworkflows/reference_assembly.nf
@@ -22,7 +22,7 @@ process map_reads{
         RightShift: ${params.poly_context}, RegexEnd: "[Aa]{${params.max_poly_run},}",
         Stranded: True,Invert: True, Tsv: "internal_priming_fail.tsv"} """
 
-        def mm2_threads = Math.min(task.cpus - 3, 1)
+        def mm2_threads = Math.max(task.cpus - 3, 1)
     """
     minimap2 -t ${mm2_threads} -ax splice ${params.minimap2_opts} ${index} ${fastq_reads}\
         | samtools view -q ${params.minimum_mapping_quality} -F 2304 -Sb -\