Merge branch 'CW-2475-sort-vcf-medaka' into 'dev'

CW-2475-sort-vcf-medaka Closes CW-2475 See merge request epi2melabs/workflows/wf-bacterial-genomes!81
epi2me-labs · Aug 15, 2023 · f90d53e · f90d53e
2 parents 8dbc8b7 + 3b696fb
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,8 @@ 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
+- Edge case where medaka variant output is unsorted and causes medaka annotate to exit
 ### Changed
 - Bumped minimum required Nextflow version to 23.04.2.
 - Now uses Medaka v1.8.2 with updated models.

diff --git a/main.nf b/main.nf
@@ -187,7 +187,8 @@ process medakaVariant {
     //       reference.* will break
     """
     medaka variant ref.fasta.gz consensus_probs*.hdf vanilla.vcf
-    medaka tools annotate vanilla.vcf ref.fasta.gz align.bam "${meta.alias}.medaka.vcf"
+    bcftools sort vanilla.vcf > vanilla.sorted.vcf
+    medaka tools annotate vanilla.sorted.vcf ref.fasta.gz align.bam "${meta.alias}.medaka.vcf"
     bgzip -i "${meta.alias}.medaka.vcf"
     bcftools stats  "${meta.alias}.medaka.vcf.gz" > "${meta.alias}.variants.stats"
     """