modules/odgi_layout

Establish 2D layouts of the graph using path-guided stochastic gradient descent. The graph must be sorted and id-compacted.

variation graphpangenome graphgfagraph layout

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

Description

Establish 2D layouts of the graph using path-guided stochastic gradient descent. The graph must be sorted and id-compacted.

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

`lay`

`meta:map`

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

`*.lay:file`

File containing a 2D layout of a pangenome graph in a binary format. Usually ends with ‘.lay’. Optional output specified by the --out FILE argument. Either this or the TSV layout output must be specified.

*.{lay}

`tsv`

`meta:map`

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

`*.tsv:file`

File containing a 2D layout of a pangenome graph in TSV format. Optional output specified by the --tsv FILE argument. Either this or the binary layout output must be specified.

*.{tsv}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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_layout

Description

Input

meta:map

graph:file

Output

lay

meta:map

*.lay:file

tsv

meta:map

*.tsv:file

versions

versions.yml:file

Tools

odgi MIT

`meta:map`

`graph:file`

`lay`

`meta:map`

`*.lay:file`

`tsv`

`meta:map`

`*.tsv:file`

`versions`

`versions.yml:file`

odgi
MIT