Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf
:file
VCF file to preprocess
*.{vcf,vcf.gz}
bed
BED file
*.bed
meta2
Groovy Map containing sample information for reference fasta e.g. [ id:‘test2’]
fasta
FASTA file of the reference genome
*.{fa,fasta}
meta3
Groovy Map containing sample information for reference fai e.g. [ id:‘test3’ ]
fasta_fai
The index of the reference FASTA
*.fai
preprocessed_vcf
*.vcf.gz
Preprocessed VCF file
versions_happy
${task.process}
:string
The process the versions were collected from
happy
The tool name
0.3.15
The expression to obtain the version of the tool
versions
Haplotype VCF comparison tools
