modules/ltrharvest

Predicts LTR retrotransposons using the parallel version of GenomeTools gt-ltrharvest utility included in the EDTA toolchain

genomicsgenomeannotationrepeattransposonsretrotransposons

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

Description

Predicts LTR retrotransposons using the parallel version of GenomeTools gt-ltrharvest utility included in the EDTA toolchain

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`fasta`
`:file`

Input genome fasta

*.{fsa,fa,fasta}

Output

name:type

description

pattern

`gff3`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.gff3`
`:file`

Predicted LTR candidates in gff3 format

*.gff3

`scn`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.scn`
`:file`

Predicted LTR candidates in scn format

*.scn

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

LTR_HARVEST_parallel
MIT

A Perl wrapper for LTR_harvest

github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel

gt
ISC

The GenomeTools genome analysis system

genometools.org genometools.org/documentation https://github.com/genometools/genometools 10.1109/TCBB.2013.68

modules/ltrharvest

Description

Input

`meta`
`:map`

`fasta`
`:file`

Output

`gff3`

`meta`
`:map`

`*.gff3`
`:file`

`scn`

`meta`
`:map`

`*.scn`
`:file`

`versions`

`versions.yml`
`:file`

Tools

LTR_HARVEST_parallel
MIT

gt
ISC

maintainer

get in touch

modules/ltrharvest

Description

Input

meta:map

fasta:file

Output

gff3

meta:map

*.gff3:file

scn

meta:map

*.scn:file

versions

versions.yml:file

Tools

LTR_HARVEST_parallel MIT

gt ISC

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`gff3`

`meta`
`:map`

`*.gff3`
`:file`

`scn`

`meta`
`:map`

`*.scn`
`:file`

`versions`

`versions.yml`
`:file`

LTR_HARVEST_parallel
MIT

gt
ISC