modules/gt_ltrharvest

Predicts LTR retrotransposons using GenomeTools gt-ltrharvest utility

genomicsgenomeannotationrepeattransposonsretrotransposons

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

Description

Predicts LTR retrotransposons using GenomeTools gt-ltrharvest utility

Input

name:type

description

pattern

`meta`
`:map`

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

`index`
`:directory`

Folder containing the suffixerator index files

suffixerator

Output

name:type

description

pattern

`tabout`

`meta`
`:map`

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

`*.tabout`
`:file`

Old tabular output by default or when -tabout yes argument is present

*.tabout

`gff3`

`meta`
`:map`

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

`*.gff3`
`:file`

GFF3 output when -tabout no argument is present

*.gff3

`fasta`

`meta`
`:map`

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

`$out_name`
`:file`

FASTA output when -out argument is present

*.{fa,fsa,fasta}

`inner_fasta`

`meta`
`:map`

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

`$outinner_name`
`:file`

FASTA output for inner regions when -outinner argument is present

*.{fa,fsa,fasta}

`versions_gt`

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

The name of the process

`genometools`
`:string`

The name of the tool

`gt --version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`genometools`
`:string`

The name of the tool

`gt --version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Tools

gt
ISC

The GenomeTools genome analysis system

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

modules/gt_ltrharvest

Description

Input

`meta`
`:map`

`index`
`:directory`

Output

`tabout`

`meta`
`:map`

`*.tabout`
`:file`

`gff3`

`meta`
`:map`

`*.gff3`
`:file`

`fasta`

`meta`
`:map`

`$out_name`
`:file`

`inner_fasta`

`meta`
`:map`

`$outinner_name`
`:file`

`versions_gt`

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

`genometools`
`:string`

`gt --version | sed '1!d;s/.* //'`
`:eval`

Topics

`versions`

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

`genometools`
`:string`

`gt --version | sed '1!d;s/.* //'`
`:eval`

Tools

gt
ISC

maintainer

get in touch

modules/gt_ltrharvest

Description

Input

meta :map

index :directory

Output

tabout

meta :map

*.tabout :file

gff3

meta :map

*.gff3 :file

fasta

meta :map

$out_name :file

inner_fasta

meta :map

$outinner_name :file

versions_gt

${task.process} :string

genometools :string

gt --version | sed '1!d;s/.* //' :eval

Topics

versions

${task.process} :string

genometools :string

gt --version | sed '1!d;s/.* //' :eval

Tools

gtISC

maintainer

get in touch

`meta`
`:map`

`index`
`:directory`

`tabout`

`meta`
`:map`

`*.tabout`
`:file`

`gff3`

`meta`
`:map`

`*.gff3`
`:file`

`fasta`

`meta`
`:map`

`$out_name`
`:file`

`inner_fasta`

`meta`
`:map`

`$outinner_name`
`:file`

`versions_gt`

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

`genometools`
`:string`

`gt --version | sed '1!d;s/.* //'`
`:eval`

`versions`

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

`genometools`
`:string`

`gt --version | sed '1!d;s/.* //'`
`:eval`

gt
ISC