name: bcftools_query description: Extracts fields from VCF or BCF files and outputs them in user-defined format. keywords: - query - variant calling - bcftools - VCF tools: - query: description: | Extracts fields from VCF or BCF files and outputs them in user-defined format. homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - vcf: type: file description: | The vcf file to be qeuried. e.g. 'file.vcf' - index: type: file description: | The tab index for the VCF file to be inspected. e.g. 'file.tbi' - regions: type: file description: | Optionally, restrict the operation to regions listed in this file. e.g. 'file.vcf' - targets: type: file description: | Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) e.g. 'file.vcf' - samples: type: file description: | Optional, file of sample names to be included or excluded. e.g. 'file.tsv' output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - vcf: type: file description: VCF query output file pattern: "*.{vcf.gz}" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@abhi18av"