modules/getorganelle_config

Downloads databases needed for running getorganelle

assemblyorganellemitochondriadownloaddatabase

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

Description

Downloads databases needed for running getorganelle

Input

name:type

description

pattern

`organelle_type`
`:string`

Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)

Output

name:type

description

pattern

`db`

`organelle_type`
`:string`

`getorganelle`
`:directory`

Downloaded database for GetOrganelle

`versions_getorganelle`

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

The name of the process

`getorganelle`
`:string`

Downloaded database for GetOrganelle

`get_organelle_config.py --version |& sed 's/^GetOrganelle 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

`getorganelle`
`:string`

Downloaded database for GetOrganelle

`get_organelle_config.py --version |& sed 's/^GetOrganelle v//'`
`:eval`

The expression to obtain the version of the tool

Tools

getorganelle
GPL v3

Get organelle genomes from genome skimming data

github.com/Kinggerm/GetOrganelle 10.1186/s13059-020-02154-5

modules/getorganelle_config

Description

Input

`organelle_type`
`:string`

Output

`db`

`organelle_type`
`:string`

`getorganelle`
`:directory`

`versions_getorganelle`

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

`getorganelle`
`:string`

`get_organelle_config.py --version |& sed 's/^GetOrganelle v//'`
`:eval`

Topics

`versions`

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

`getorganelle`
`:string`

`get_organelle_config.py --version |& sed 's/^GetOrganelle v//'`
`:eval`

Tools

getorganelle
GPL v3

maintainer

get in touch

modules/getorganelle_config

Description

Input

organelle_type:string

Output

db

organelle_type:string

getorganelle:directory

versions_getorganelle

${task.process}:string

getorganelle:string

get_organelle_config.py --version |& sed 's/^GetOrganelle v//':eval

Topics

versions

${task.process}:string

getorganelle:string

get_organelle_config.py --version |& sed 's/^GetOrganelle v//':eval

Tools

getorganelle GPL v3

maintainer

get in touch

`organelle_type`
`:string`

`db`

`organelle_type`
`:string`

`getorganelle`
`:directory`

`versions_getorganelle`

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

`getorganelle`
`:string`

`get_organelle_config.py --version |& sed 's/^GetOrganelle v//'`
`:eval`

`versions`

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

`getorganelle`
`:string`

`get_organelle_config.py --version |& sed 's/^GetOrganelle v//'`
`:eval`

getorganelle
GPL v3