Normalize VCF file
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf
:file
The vcf file to be normalized e.g. ‘file1.vcf’
*.{vcf,vcf.gz}
tbi
An optional index of the VCF file (for when the VCF is compressed)
*.vcf.gz.tbi
meta2
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta
FASTA reference file
*.{fasta,fa}
*.{vcf,vcf.gz,bcf,bcf.gz}
One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file
*.tbi
Alternative VCF file index
csi
*.csi
Default VCF file index
versions_bcftools
${task.process}
:string
The process the versions were collected from
bcftools
The tool name
bcftools --version | sed '1!d; s/^.*bcftools //'
The command used to generate the version of the tool
versions
Normalize VCF files.
