Merge branch 'CW-3378' into 'dev'

CW-3378 dot plot sensitivity

See merge request epi2melabs/workflows/wf-clone-validation!187

CHANGELOG.md

@@ -4,7 +4,9 @@ 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]
+## [v1.1.0]
+### Changed
+- Ensure repetitive regions are marked on the dot plot by reducing the threshold for suppressing repeats inside exact matches.
 ### Added
 - `--large_construct` parameter for assembly of larger constructs including Bacterial Artificial Constructs(50,000-300,000bps).
 

main.nf

@@ -353,11 +353,13 @@ process assemblyMafs {
         tuple val(sample_id), path("assembly.fasta")
     output:
         tuple val(sample_id), path("${sample_id}.assembly.maf"), emit: assembly_maf
-    // set -m(multiplicity) to 1000 to increase sensitivity from default of 10
-    // for assemblies these small computational cost is low
+    // set -m(multiplicity) to 10000 to increase sensitivity from default of 10
+    // for assemblies this small computational cost is low
+    // reduce offset distance for suppressing repeats inside exact matches -w 
+    // from default of 1000 to 10.
     """
     lastdb db.lastdb "assembly.fasta"
-    lastal -m10000 db.lastdb "assembly.fasta" > "${sample_id}.assembly.maf"
+    lastal -m 10000 -w 10 db.lastdb "assembly.fasta" > "${sample_id}.assembly.maf"
   
     """
 }

nextflow.config

@@ -59,7 +59,7 @@ manifest {
     description     = 'De-novo reconstruction of synthetic plasmid sequences.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v1.0.0'
+    version         = 'v1.1.0'
 }
 
 epi2melabs {