Nextflow Registry | nf-core/gatk4/shiftfasta@0.0.0-6c4ed3a

nf-core/gatk4/shiftfasta @ 0.0.0-6c4ed3a

Create a fasta with the bases shifted by offset

gatk4 mitochondria shiftchain shiftfasta shiftintervals

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @ramprasadn

Maintainers: @ramprasadn

Create a fasta with the bases shifted by offset

Add the following snippet to your workflow script to include this module.

include { GATK4_SHIFTFASTA } from 'nf-core/gatk4/shiftfasta'

MIT License

Process

`Name`	`GATK4_SHIFTFASTA`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing reference information e.g. [ id:'test' ]
`fasta` file	fasta file `*.{fa,fasta}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test' ]
`fasta_fai` file	index for fasta file `*.{fai}`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'test' ]
`dict` file	sequence dictionary file `*.{dict}`

Output 7 channels

#1 dict tuple

`meta` map	Groovy Map containing fasta information e.g. [ id:'test' ]
`*_shift.dict` file	sequence dictionary file `*.{dict}`

#2 shift_fa tuple

`meta` map	Groovy Map containing fasta information e.g. [ id:'test' ]
`*_shift.fasta` file	Shifted fasta file `*.{fa,fasta}`

#3 intervals tuple

`meta` map	Groovy Map containing fasta information e.g. [ id:'test' ]
`*.intervals` file	Intervals file for the fasta file `*.{intervals}`

#4 shift_fai tuple

`meta` map	Groovy Map containing fasta information e.g. [ id:'test' ]
`*_shift.fasta.fai` file	Index file for the shifted fasta file `*.{fai}`

#5 versions_gatk4 tuple

`${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

#6 shift_intervals tuple

`meta` map	Groovy Map containing fasta information e.g. [ id:'test' ]
`*.shifted.intervals` file	Intervals file for the shifted fasta file `*.{shifted.intervals}`

#7 shift_back_chain tuple

`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}`

Tool	Description	Homepage
gatk4	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.	https://gatk.broadinstitute.org/hc/en-us

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:20:32 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fshiftfasta/0.0.0-6c4ed3a/download