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}

`s: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}

`s:file`

Intervals file for the shifted fasta file

*.{shifted.intervals}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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

modules/gatk4_shiftfasta

Description

Input

meta:map

fasta:file

meta2:map

fasta_fai:file

meta3:map

dict:file

Output

shift_fa

meta:map

*_shift.fasta:file

shift_fai

meta:map

*_shift.fasta.fai:file

shift_back_chain

meta:map

*_shift.back_chain:file

dict

meta:map

*_shift.dict:file

intervals

meta:map

*.intervals:file

s:file

shift_intervals

meta:map

*.shifted.intervals:file

s:file

versions

versions.yml:file

Tools

gatk4 Apache-2.0

`meta:map`

`fasta:file`

`meta2:map`

`fasta_fai:file`

`meta3:map`

`dict:file`

`shift_fa`

`meta:map`

`*_shift.fasta:file`

`shift_fai`

`meta:map`

`*_shift.fasta.fai:file`

`shift_back_chain`

`meta:map`

`*_shift.back_chain:file`

`dict`

`meta:map`

`*_shift.dict:file`

`intervals`

`meta:map`

`*.intervals:file`

`s:file`

`shift_intervals`

`meta:map`

`*.shifted.intervals:file`

`s:file`

`versions`

`versions.yml:file`

gatk4
Apache-2.0