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add bcftools sort operation #44

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add bcftools sort operation #44

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a212fa0
add bcftools sort operation
priesgo Feb 6, 2023
b97d2db
hey
priesgo Jan 25, 2024
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1 change: 0 additions & 1 deletion main.nf
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion modules/04_variant_calling.nf
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -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'
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