modules/odgi_sort

Apply different kind of sorting algorithms to a graph. The most prominent one is the PG-SGD sorting algorithm.

variation graphpangenome graphgfagraph layout

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

Description

Apply different kind of sorting algorithms to a graph. The most prominent one is the PG-SGD sorting algorithm.

Input

name:type

description

pattern

`meta`
`:map`

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

`graph`
`:file`

Pangenome graph in GFA v1.0 format or in ODGI binary format

*.{gfa,og}

Output

name:type

description

pattern

`sorted_graph`

`meta`
`:map`

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

`*.og`
`:file`

1D sorted pangenome graph in ODGI binary format

*.{og}

`versions_odgi`

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

The name of the process

`odgi`
`:string`

The name of the tool

`odgi version | sed 's/^v//; 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

`odgi`
`:string`

The name of the tool

`odgi version | sed 's/^v//; s/-.*//'`
`:eval`

The expression to obtain the version of the tool

Tools

odgi
MIT

An optimized dynamic genome/graph implementation

github.com/pangenome/odgi odgi.readthedocs.io/en/latest https://github.com/pangenome/odgi 10.1093/bioinformatics/btac308

modules/odgi_sort

Description

Input

`meta`
`:map`

`graph`
`:file`

Output

`sorted_graph`

`meta`
`:map`

`*.og`
`:file`

`versions_odgi`

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

`odgi`
`:string`

`odgi version | sed 's/^v//; s/-.*//'`
`:eval`

Topics

`versions`

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

`odgi`
`:string`

`odgi version | sed 's/^v//; s/-.*//'`
`:eval`

Tools

odgi
MIT

included in

maintainer

get in touch

modules/odgi_sort

Description

Input

meta :map

graph :file

Output

sorted_graph

meta :map

*.og :file

versions_odgi

${task.process} :string

odgi :string

odgi version | sed 's/^v//; s/-.*//' :eval

Topics

versions

${task.process} :string

odgi :string

odgi version | sed 's/^v//; s/-.*//' :eval

Tools

odgiMIT

included in

maintainer

get in touch

`meta`
`:map`

`graph`
`:file`

`sorted_graph`

`meta`
`:map`

`*.og`
`:file`

`versions_odgi`

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

`odgi`
`:string`

`odgi version | sed 's/^v//; s/-.*//'`
`:eval`

`versions`

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

`odgi`
`:string`

`odgi version | sed 's/^v//; s/-.*//'`
`:eval`

odgi
MIT