From 73a2b45268e738ed5bdd74e0d5443a7ca669f1ac Mon Sep 17 00:00:00 2001
From: Biowilko <sam1.wilkinson1@gmail.com>
Date: Tue, 3 Sep 2024 18:33:40 +0100
Subject: [PATCH] Apply bcftools fix to both rounds of consensus building

---
 modules/illumina.nf | 2 +-
 nextflow.config     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/illumina.nf b/modules/illumina.nf
index ba702a3..056a7cc 100644
--- a/modules/illumina.nf
+++ b/modules/illumina.nf
@@ -264,7 +264,7 @@ process callConsensusFreebayes {
     done
 
     # apply ambiguous variants first using IUPAC codes. this variant set cannot contain indels or the subsequent step will break
-    bcftools consensus -f ${ref} -I ${sampleName}.ambiguous.norm.vcf.gz > ${sampleName}.ambiguous.fa
+    bcftools consensus -s - -f ${ref} -I ${sampleName}.ambiguous.norm.vcf.gz > ${sampleName}.ambiguous.fa
 
     # Get viral contig name from reference
     CTG_NAME=\$(head -n1 ${ref} | sed 's/>//')
diff --git a/nextflow.config b/nextflow.config
index d1a9373..3cc794e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -5,7 +5,7 @@ manifest {
   description = 'Epi2me compatible Nextflow pipeline for processing ARTIC tiling amplicon Illumina sequencing reads from monkeypox virus (MPXV) samples.'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'
-  version = '1.0.12'
+  version = '1.0.13'
 }
 
 // Load base.config by default for all pipelines