From a212fa03b92e535680d86a64d2c2124ebf46b48c Mon Sep 17 00:00:00 2001
From: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com>
Date: Mon, 6 Feb 2023 22:35:14 +0000
Subject: [PATCH 1/2] add bcftools sort operation

---
 modules/04_variant_calling.nf | 2 +-
 nextflow.config               | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/04_variant_calling.nf b/modules/04_variant_calling.nf
index b6c8fc0..2e92924 100644
--- a/modules/04_variant_calling.nf
+++ b/modules/04_variant_calling.nf
@@ -75,7 +75,7 @@ process VARIANT_CALLING_LOFREQ {
     --min-mq ${params.min_mapping_quality} \
     --ref ${reference} \
     --call-indels \
-    <( lofreq indelqual --dindel --ref ${reference} ${bam} ) | bgzip > ${name}.lofreq.vcf.gz
+    <( lofreq indelqual --dindel --ref ${reference} ${bam} ) | bcftools sort | bgzip > ${name}.lofreq.vcf.gz
 
     # NOTE: adding the tabix index is a dirty fix to deal with LoFreq VCF missing the chromosome in the header
     bcftools index ${name}.lofreq.vcf.gz
diff --git a/nextflow.config b/nextflow.config
index cba16a1..ae09152 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -62,7 +62,7 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 cleanup = true
 conda.createTimeout = '1 h'
 
-VERSION = '0.17.0'
+VERSION = '0.17.1'
 
 manifest {
   name = 'TRON-Bioinformatics/covigator-ngs-pipeline'

From b97d2db7fbee67b94d1d5fd3eac26bf341683451 Mon Sep 17 00:00:00 2001
From: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com>
Date: Thu, 25 Jan 2024 12:43:00 +0000
Subject: [PATCH 2/2] hey

---
 main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/main.nf b/main.nf
index 93beb95..9f701d4 100755
--- a/main.nf
+++ b/main.nf
@@ -14,7 +14,6 @@ include { VARIANT_ANNOTATION; VARIANT_SARSCOV2_ANNOTATION;
 include { PANGOLIN_LINEAGE; VCF2FASTA } from './modules/07_lineage_annotation'
 include { BGZIP } from './modules/08_compress_vcf'
 
-
 params.help= false
 
 params.fastq1 = false