Extracts fields from VCF or BCF files and outputs them in user-defined format.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf
:file
The vcf file to be queried.
*.{vcf.gz, vcf}
tbi
The tab index for the VCF file to be inspected.
*.tbi
regions
Optionally, restrict the operation to regions listed in this file.
targets
Optionally, restrict the operation to regions listed in this file (doesn’t rely upon index files)
samples
Optional, file of sample names to be included or excluded. e.g. ‘file.tsv’
output
*.${suffix}
BCFTools query output file
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
