modules/gangstr

GangSTR is a tool for genome-wide profiling tandem repeats from short reads.

gangstrSTRbamcramvcf

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

Description

GangSTR is a tool for genome-wide profiling tandem repeats from short reads.

Input

name:type

description

pattern

`meta`
`:map`

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

`alignment_files`
`:file`

Alignment files

`alignment_indices`
`:file`

The index/indices of the BAM/CRAM file(s)

*.{bai,crai}

`ref_regions`
`:file`

A reference set of regions to genotype in a BED-like format. The file should have following columns:

The name of the chromosome on which the STR is located
The start position of the STR on its chromosome
The end position of the STR on its chromosome
The motif length
The repeat motif

*.bed

`fasta`
`:file`

The reference FASTA file

*.{fasta,fa}

`fasta_fai`
`:file`

The index of the reference FASTA file

*.fai

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

`*.vcf.gz`
`:file`

The resulting VCF file containing the genotypes

*.vcf.gz

`index`

`meta`
`:map`

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

`*.vcf.gz.tbi`
`:file`

The resulting index of the VCF file containing the genotypes

*.vcf.gz.tbi

`samplestats`

`meta`
`:map`

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

`*.samplestats.tab`
`:file`

A tab-delimited file containing statistics for each sample

*.tab

`versions_gangstr`

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

Task process name

`gangstr`
`:string`

Software name

`GangSTR --version 2>&1`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

Task process name

`gangstr`
`:string`

Software name

`GangSTR --version 2>&1`
`:eval`

The expression to obtain the version of the tool

Tools

gangstr
GPL v3-or-later

GangSTR is a tool for genome-wide profiling tandem repeats from short reads.

github.com/gymreklab/GangSTR 10.1093/nar/gkz501

modules/gangstr

Description

Input

`meta`
`:map`

`alignment_files`
`:file`

`alignment_indices`
`:file`

`ref_regions`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`index`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`samplestats`

`meta`
`:map`

`*.samplestats.tab`
`:file`

`versions_gangstr`

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

`gangstr`
`:string`

`GangSTR --version 2>&1`
`:eval`

Topics

`versions`

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

`gangstr`
`:string`

`GangSTR --version 2>&1`
`:eval`

Tools

gangstr
GPL v3-or-later

maintainer

get in touch

modules/gangstr

Description

Input

meta:map

alignment_files:file

alignment_indices:file

ref_regions:file

fasta:file

fasta_fai:file

Output

vcf

meta:map

*.vcf.gz:file

index

meta:map

*.vcf.gz.tbi:file

samplestats

meta:map

*.samplestats.tab:file

versions_gangstr

${task.process}:string

gangstr:string

GangSTR --version 2>&1:eval

Topics

versions

${task.process}:string

gangstr:string

GangSTR --version 2>&1:eval

Tools

gangstr GPL v3-or-later

maintainer

get in touch

`meta`
`:map`

`alignment_files`
`:file`

`alignment_indices`
`:file`

`ref_regions`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`index`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`samplestats`

`meta`
`:map`

`*.samplestats.tab`
`:file`

`versions_gangstr`

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

`gangstr`
`:string`

`GangSTR --version 2>&1`
`:eval`

`versions`

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

`gangstr`
`:string`

`GangSTR --version 2>&1`
`:eval`

gangstr
GPL v3-or-later