Sorts vcf files
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf{:bash}
:file
VCF file
*.{vcf,vcf.gz}
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta{:bash}
Reference genome fasta file
*.{fasta,fa}
meta3{:bash}
dict{:bash}
Reference genome dictionary file
*.{dict}
*_sorted.vcf.gz{:bash}
Sorted VCF file
*.{vcf}
versions_picard{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
picard{:bash}
The tool name
picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'{:bash}
The command used to generate the version of the tool
versions{:bash}
Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format
