name: bcftools_reheader description: Reheader a VCF file keywords: - reheader - vcf - update header tools: - reheader: description: | Modify header of VCF/BCF files, change sample names. homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://samtools.github.io/bcftools/bcftools.html#reheader doi: 10.1093/gigascience/giab008 licence: ["MIT"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - vcf: type: file description: VCF/BCF file pattern: "*.{vcf.gz,vcf,bcf}" - fai: type: file description: Fasta index to update header sequences with pattern: "*.{fai}" - header: type: file description: New header to add to the VCF pattern: "*.{header.txt}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - vcf: type: file description: VCF with updated header pattern: "*.{vcf.gz}" authors: - "@bjohnnyd"