Apply bcftools fix to both rounds of consensus building

artic-network · Sep 3, 2024 · 73a2b45 · 73a2b45
1 parent a574880
commit 73a2b45
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git 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
@@ -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