modules/ltrfinder

Finds full-length LTR retrotranspsons in genome sequences using the parallel version of LTR_Finder

genomicsannotationparallelrepeatlong terminal retrotransposonretrotransposon

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

Description

Finds full-length LTR retrotranspsons in genome sequences using the parallel version of LTR_Finder

Input

name:type

description

pattern

`meta`
`:map`

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

`fasta`
`:file`

Genome sequences in fasta format

*.{fsa,fa,fasta}

Output

name:type

description

pattern

`scn`

`meta`
`:map`

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

`*.scn`
`:file`

Annotation in LTRharvest or LTR_FINDER format

*.scn

`gff`

`meta`
`:map`

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

`*.gff3`
`:file`

Annotation in gff3 format

*.gff3

`versions_ltr_finder_parallel`

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

The name of the process

`LTR_FINDER_parallel`
`:string`

The name of the tool

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

The expression to obtain the version of the tool

`versions_ltr_finder`

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

The name of the process

`ltr_finder`
`:string`

The name of the tool

`ltr_finder -h 2>&1 | sed -n 's/ltr_finder v//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_FINDER_parallel`
`:string`

The name of the tool

`LTR_FINDER_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

`ltr_finder`
`:string`

The name of the tool

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

The expression to obtain the version of the tool

Tools

LTR_FINDER_parallel
MIT

A Perl wrapper for LTR_FINDER

github.com/oushujun/LTR_FINDER_parallel 10.1186/s13100-019-0193-0

LTR_Finder
MIT

An efficient program for finding full-length LTR retrotranspsons in genome sequences

github.com/xzhub/LTR_Finder 10.1093/nar/gkm286

modules/ltrfinder

Description

Input

`meta`
`:map`

`fasta`
`:file`

Output

`scn`

`meta`
`:map`

`*.scn`
`:file`

`gff`

`meta`
`:map`

`*.gff3`
`:file`

`versions_ltr_finder_parallel`

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

`LTR_FINDER_parallel`
`:string`

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

`versions_ltr_finder`

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

`ltr_finder`
`:string`

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

Topics

`versions`

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

`LTR_FINDER_parallel`
`:string`

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

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

`ltr_finder`
`:string`

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

Tools

LTR_FINDER_parallel
MIT

LTR_Finder
MIT

maintainer

get in touch

modules/ltrfinder

Description

Input

meta :map

fasta :file

Output

scn

meta :map

*.scn :file

gff

meta :map

*.gff3 :file

versions_ltr_finder_parallel

${task.process} :string

LTR_FINDER_parallel :string

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

versions_ltr_finder

${task.process} :string

ltr_finder :string

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

Topics

versions

${task.process} :string

LTR_FINDER_parallel :string

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

${task.process} :string

ltr_finder :string

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

Tools

LTR_FINDER_parallelMIT

LTR_FinderMIT

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`scn`

`meta`
`:map`

`*.scn`
`:file`

`gff`

`meta`
`:map`

`*.gff3`
`:file`

`versions_ltr_finder_parallel`

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

`LTR_FINDER_parallel`
`:string`

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

`versions_ltr_finder`

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

`ltr_finder`
`:string`

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

`versions`

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

`LTR_FINDER_parallel`
`:string`

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

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

`ltr_finder`
`:string`

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

LTR_FINDER_parallel
MIT

LTR_Finder
MIT