Estimate repeat sizes using NGS data
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
BAM/CRAM file
*.{bam,cram}
bai{:bash}
Index of BAM/CRAM file
*.{bai,crai}
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘test’ ]
fasta{:bash}
Reference genome
*.{fna,fa,fasta}
meta3{:bash}
fasta_fai{:bash}
Reference genome index
*.fai
meta4{:bash}
variant_catalog{:bash}
JSON file with repeat expansion sites to genotype
*.json
vcf{:bash}
Groovy Map containing sample information e.g. [ id:‘test’, gender:‘female’ ]
*.vcf.gz{:bash}
VCF with repeat expansions
*.vcf.gz
json{:bash}
*.json.gz{:bash}
JSON with repeat expansions
*.json.gz
*_realigned.bam{:bash}
versions_expansionhunter{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
expansionhunter{:bash}
The tool name
ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p'{:bash}
:eval
The expression to obtain the version of the tool
versions_bgzip{:bash}
bgzip{:bash}
bgzip --version | sed '1!d;s/.* //'{:bash}
versions{:bash}
A tool for estimating repeat sizes
