Reheader a VCF file
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf{:bash}
:file
VCF/BCF file
*.{vcf.gz,vcf,bcf}
header{:bash}
New header to add to the VCF
*.{header.txt}
samples{:bash}
File containing sample names to update (one sample per line)
*.{samples.txt}
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fai{:bash}
Fasta index to update header sequences with
*.{fai}
*.{vcf,vcf.gz,bcf,bcf.gz}{:bash}
VCF with updated header, bgzipped per default
*.{vcf,vcf.gz,bcf,bcf.gz}
index{:bash}
*.{csi,tbi}{:bash}
Index of VCF with updated header
*.{csi,tbi}
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}
Modify header of VCF/BCF files, change sample names.
