modules/expansionhunter

Estimate repeat sizes using NGS data

STRrepeat_expansionsbamcramvcfjson

https://github.com/nf-core/modules/[...]/modules/nf-core/expansionhunter

Description

Estimate repeat sizes using NGS data

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`bam`
`:file`

BAM/CRAM file

*.{bam,cram}

`bai`
`:file`

Index of BAM/CRAM file

*.{bai,crai}

`meta2`
`:map`

Groovy Map containing reference information e.g. [ id:‘test’ ]

`fasta`
`:file`

Reference genome

*.{fna,fa,fasta}

`meta3`
`:map`

Groovy Map containing reference information e.g. [ id:‘test’ ]

`fasta_fai`
`:file`

Reference genome index

*.fai

`meta4`
`:map`

Groovy Map containing reference information e.g. [ id:‘test’ ]

`variant_catalog`
`:file`

JSON file with repeat expansion sites to genotype

*.json

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, gender:‘female’ ]

`*.vcf.gz`
`:file`

VCF with repeat expansions

*.vcf.gz

`json`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, gender:‘female’ ]

`*.json.gz`
`:file`

JSON with repeat expansions

*.json.gz

`bam`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, gender:‘female’ ]

`*_realigned.bam`
`:file`

BAM/CRAM file

*.{bam,cram}

`versions_expansionhunter`

`${task.process}`
`:string`

The process the versions were collected from

`expansionhunter`
`:string`

The tool name

`ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p'`
`:eval`

The expression to obtain the version of the tool

`versions_bgzip`

`${task.process}`
`:string`

The process the versions were collected from

`bgzip`
`:string`

The tool name

`bgzip --version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`expansionhunter`
`:string`

The tool name

`ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p'`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The process the versions were collected from

`bgzip`
`:string`

The tool name

`bgzip --version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Tools

expansionhunter
Apache-2.0

A tool for estimating repeat sizes

github.com/Illumina/ExpansionHunter github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md 10.1093/bioinformatics/btz431

modules/expansionhunter

Description

Input

meta:map

bam:file

bai:file

meta2:map

fasta:file

meta3:map

fasta_fai:file

meta4:map

variant_catalog:file

Output

vcf

meta:map

*.vcf.gz:file

json

meta:map

*.json.gz:file

bam

meta:map

*_realigned.bam:file

versions_expansionhunter

${task.process}:string

expansionhunter:string

ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p':eval

versions_bgzip

${task.process}:string

bgzip:string

bgzip --version | sed '1!d;s/.* //':eval

Topics

versions

${task.process}:string

expansionhunter:string

ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p':eval

${task.process}:string

bgzip:string

bgzip --version | sed '1!d;s/.* //':eval

Tools

expansionhunter Apache-2.0

included in

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fasta_fai`
`:file`

`meta4`
`:map`

`variant_catalog`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`json`

`meta`
`:map`

`*.json.gz`
`:file`

`bam`

`meta`
`:map`

`*_realigned.bam`
`:file`

`versions_expansionhunter`

`${task.process}`
`:string`

`expansionhunter`
`:string`

`ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p'`
`:eval`

`versions_bgzip`

`${task.process}`
`:string`

`bgzip`
`:string`

`bgzip --version | sed '1!d;s/.* //'`
`:eval`

`versions`

`${task.process}`
`:string`

`expansionhunter`
`:string`

`ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p'`
`:eval`

`${task.process}`
`:string`

`bgzip`
`:string`

`bgzip --version | sed '1!d;s/.* //'`
`:eval`

expansionhunter
Apache-2.0