modules/repeatmodeler_repeatmodeler

Performs de novo transposable element (TE) family identification with RepeatModeler

genomicsfastarepeattransposable element

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

Description

Performs de novo transposable element (TE) family identification with RepeatModeler

Input

name:type

description

pattern

`meta:map`

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

`db:file`

RepeatModeler database files generated with REPEATMODELER_BUILDDATABASE

*

Output

name:type

description

pattern

`fasta`

`meta:map`

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

`*.fa:file`

Consensus repeat sequences

*.fa

`stk`

`meta:map`

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

`*.stk:file`

Seed alignments

*.stk

`log`

`meta:map`

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

`*.log:file`

A summarized log of the run

*.log

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

repeatmodeler
Open Software License v2.1

RepeatModeler is a de-novo repeat family identification and modeling package.

github.com/Dfam-consortium/RepeatModeler

modules/repeatmodeler_repeatmodeler

Description

Input

`meta:map`

`db:file`

Output

`fasta`

`meta:map`

`*.fa:file`

`stk`

`meta:map`

`*.stk:file`

`log`

`meta:map`

`*.log:file`

`versions`

`versions.yml:file`

Tools

repeatmodeler
Open Software License v2.1

maintainer

get in touch

modules/repeatmodeler_repeatmodeler

Description

Input

meta:map

db:file

Output

fasta

meta:map

*.fa:file

stk

meta:map

*.stk:file

log

meta:map

*.log:file

versions

versions.yml:file

Tools

repeatmodeler Open Software License v2.1

maintainer

get in touch

`meta:map`

`db:file`

`fasta`

`meta:map`

`*.fa:file`

`stk`

`meta:map`

`*.stk:file`

`log`

`meta:map`

`*.log:file`

`versions`

`versions.yml:file`

repeatmodeler
Open Software License v2.1