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_ltr_harvest_parallel`

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

The name of the process

`LTR_HARVEST_parallel`
`:string`

The name of the tool

`LTR_HARVEST_parallel -h 2>&1 | sed -n 's/Version: v//p'`
`:eval`

The expression to obtain the version of the tool

`versions_genometools`

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

The name of the process

`genometools`
`:string`

The name of the tool

`gt --version | sed -n 's/gt (GenomeTools) //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

`LTR_HARVEST_parallel`
`:string`

The name of the tool

`LTR_HARVEST_parallel -h 2>&1 | sed -n 's/Version: v//p'`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`genometools`
`:string`

The name of the tool

`gt --version | sed -n 's/gt (GenomeTools) //p'`
`:eval`

The expression to obtain the version of the tool

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_ltr_harvest_parallel`

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

`LTR_HARVEST_parallel`
`:string`

`LTR_HARVEST_parallel -h 2>&1 | sed -n 's/Version: v//p'`
`:eval`

`versions_genometools`

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

`genometools`
`:string`

`gt --version | sed -n 's/gt (GenomeTools) //p'`
`:eval`

Topics

`versions`

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

`LTR_HARVEST_parallel`
`:string`

`LTR_HARVEST_parallel -h 2>&1 | sed -n 's/Version: v//p'`
`:eval`

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

`genometools`
`:string`

`gt --version | sed -n 's/gt (GenomeTools) //p'`
`:eval`

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_ltr_harvest_parallel

${task.process} :string

LTR_HARVEST_parallel :string

LTR_HARVEST_parallel -h 2>&1 | sed -n 's/Version: v//p' :eval

versions_genometools

${task.process} :string

genometools :string

gt --version | sed -n 's/gt (GenomeTools) //p' :eval

Topics

versions

${task.process} :string

LTR_HARVEST_parallel :string

LTR_HARVEST_parallel -h 2>&1 | sed -n 's/Version: v//p' :eval

${task.process} :string

genometools :string

gt --version | sed -n 's/gt (GenomeTools) //p' :eval

Tools

LTR_HARVEST_parallelMIT

gtISC

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`gff3`

`meta`
`:map`

`*.gff3`
`:file`

`scn`

`meta`
`:map`

`*.scn`
`:file`

`versions_ltr_harvest_parallel`

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

`LTR_HARVEST_parallel`
`:string`

`LTR_HARVEST_parallel -h 2>&1 | sed -n 's/Version: v//p'`
`:eval`

`versions_genometools`

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

`genometools`
`:string`

`gt --version | sed -n 's/gt (GenomeTools) //p'`
`:eval`

`versions`

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

`LTR_HARVEST_parallel`
`:string`

`LTR_HARVEST_parallel -h 2>&1 | sed -n 's/Version: v//p'`
`:eval`

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

`genometools`
`:string`

`gt --version | sed -n 's/gt (GenomeTools) //p'`
`:eval`

LTR_HARVEST_parallel
MIT

gt
ISC