Extracts fields from VCF or BCF files and outputs them in user-defined format.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf{:bash}
:file
The vcf file to be queried.
*.{vcf.gz, vcf}
tbi{:bash}
The tab index for the VCF file to be inspected.
*.tbi
regions{:bash}
Optionally, restrict the operation to regions listed in this file.
targets{:bash}
Optionally, restrict the operation to regions listed in this file (doesn’t rely upon index files)
samples{:bash}
Optional, file of sample names to be included or excluded. e.g. ‘file.tsv’
output{:bash}
*.${suffix}{:bash}
BCFTools query output file
versions_bcftools{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
bcftools{:bash}
The tool name
bcftools --version | sed '1!d; s/^.*bcftools //'{:bash}
The command used to generate the version of the tool
versions{:bash}
