modules/agat_spstatistics

Provides different type of statistics in text format from a GFF/GTF annotation file

genomegffgtfstatistics

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

Description

Provides different type of statistics in text format from a GFF/GTF annotation file

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`gff`
`:file`

Annotation file in GFF3/GTF format

*.{gff, gtf}

Output

name:type

description

pattern

`stats_txt`

`meta`
`:map`

Groovy Map containing sample information

`*.txt`
`:file`

Output of Statistics execution

*.{txt}

`versions_agat`

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

The name of the process

`agat`
`:string`

The name of the tool

`agat --version | sed 's/v//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`agat`
`:string`

The name of the tool

`agat --version | sed 's/v//'`
`:eval`

The expression to obtain the version of the tool

Tools

agat
GPL v3

AGAT is a toolkit for manipulation and getting information from GFF/GTF files

github.com/NBISweden/AGAT agat.readthedocs.io https://github.com/NBISweden/AGAT 10.5281/zenodo.3552717

modules/agat_spstatistics

Description

Input

`meta`
`:map`

`gff`
`:file`

Output

`stats_txt`

`meta`
`:map`

`*.txt`
`:file`

`versions_agat`

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

`agat`
`:string`

`agat --version | sed 's/v//'`
`:eval`

Topics

`versions`

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

`agat`
`:string`

`agat --version | sed 's/v//'`
`:eval`

Tools

agat
GPL v3

included in

maintainers

get in touch

modules/agat_spstatistics

Description

Input

meta:map

gff:file

Output

stats_txt

meta:map

*.txt:file

versions_agat

${task.process}:string

agat:string

agat --version | sed 's/v//':eval

Topics

versions

${task.process}:string

agat:string

agat --version | sed 's/v//':eval

Tools

agat GPL v3

included in

maintainers

get in touch

`meta`
`:map`

`gff`
`:file`

`stats_txt`

`meta`
`:map`

`*.txt`
`:file`

`versions_agat`

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

`agat`
`:string`

`agat --version | sed 's/v//'`
`:eval`

`versions`

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

`agat`
`:string`

`agat --version | sed 's/v//'`
`:eval`

agat
GPL v3