modules/gatk4_shiftfasta

Create a fasta with the bases shifted by offset

gatk4mitochondriashiftchainshiftfastashiftintervals

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/shiftfasta

Description

Create a fasta with the bases shifted by offset

Input

name:type

description

pattern

`meta`
`:map`

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

`fasta`
`:file`

fasta file

*.{fa,fasta}

`meta2`
`:map`

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

`fasta_fai`
`:file`

index for fasta file

*.{fai}

`meta3`
`:map`

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

`dict`
`:file`

sequence dictionary file

*.{dict}

Output

name:type

description

pattern

`shift_fa`

`meta`
`:map`

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

`*_shift.fasta`
`:file`

Shifted fasta file

*.{fa,fasta}

`shift_fai`

`meta`
`:map`

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

`*_shift.fasta.fai`
`:file`

Index file for the shifted fasta file

*.{fai}

`shift_back_chain`

`meta`
`:map`

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

`*_shift.back_chain`
`:file`

The shiftback chain file to use when lifting over

*.{back_chain}

`dict`

`meta`
`:map`

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

`*_shift.dict`
`:file`

sequence dictionary file

*.{dict}

`intervals`

`meta`
`:map`

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

`*.intervals`
`:file`

Intervals file for the fasta file

*.{intervals}

`shift_intervals`

`meta`
`:map`

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

`*.shifted.intervals`
`:file`

Intervals file for the shifted fasta file

*.{shifted.intervals}

`versions_gatk4`

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

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Tools

gatk4
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590