modules/expansionhunterdenovo_merge

Merge STR profiles into a multi-sample STR profile

expansionhunterdenovomergestr

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

Description

Merge STR profiles into a multi-sample STR profile

Input

name:type

description

pattern

`meta`
`:map`

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

`manifest`
`:file`

A tab-delimited file containing the sample name, whether it’s case or control and the paths to the corresponding STR profiles. See here for an example: https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/06_Merging_profiles.md#manifest-files

*.{tsv,txt}

`meta2`
`:map`

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

`fasta`
`:file`

The reference FASTA file

*.{fasta,fa}

`fasta_fai`
`:file`

The index of the reference FASTA file

*.fai

Output

name:type

description

pattern

`merged_profiles`

`meta`
`:map`

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

`*.multisample_profile.json`
`:file`

The merged STR profiles

*.multisample_profile.json

`versions_expansionhunterdenovo`

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

The name of the process

`expansionhunterdenovo`
`:string`

The name of the tool

`ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`expansionhunterdenovo`
`:string`

The name of the tool

`ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//'`
`:eval`

The expression to obtain the version of the tool

Tools

expansionhunterdenovo
Apache License 2.0

ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).

github.com/Illumina/ExpansionHunterDenovo github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/00_Introduction.md https://github.com/Illumina/ExpansionHunterDenovo

modules/expansionhunterdenovo_merge

Description

Input

`meta`
`:map`

`manifest`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fasta_fai`
`:file`

Output

`merged_profiles`

`meta`
`:map`

`*.multisample_profile.json`
`:file`

`versions_expansionhunterdenovo`

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

`expansionhunterdenovo`
`:string`

`ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//'`
`:eval`

Topics

`versions`

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

`expansionhunterdenovo`
`:string`

`ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//'`
`:eval`

Tools

expansionhunterdenovo
Apache License 2.0

maintainer

get in touch

modules/expansionhunterdenovo_merge

Description

Input

meta:map

manifest:file

meta2:map

fasta:file

fasta_fai:file

Output

merged_profiles

meta:map

*.multisample_profile.json:file

versions_expansionhunterdenovo

${task.process}:string

expansionhunterdenovo:string

ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//':eval

Topics

versions

${task.process}:string

expansionhunterdenovo:string

ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//':eval

Tools

expansionhunterdenovo Apache License 2.0

maintainer

get in touch

`meta`
`:map`

`manifest`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fasta_fai`
`:file`

`merged_profiles`

`meta`
`:map`

`*.multisample_profile.json`
`:file`

`versions_expansionhunterdenovo`

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

`expansionhunterdenovo`
`:string`

`ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//'`
`:eval`

`versions`

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

`expansionhunterdenovo`
`:string`

`ExpansionHunterDenovo --help |& sed '1!d;s/ExpansionHunter Denovo v//'`
`:eval`

expansionhunterdenovo
Apache License 2.0