Nextflow Registry | nf-core/getorganelle/fromreads@0.0.0-6c4ed3a

nf-core/getorganelle/fromreads @ 0.0.0-6c4ed3a

Assembles organelle genomes from genomic data

assembly organelle mitochondria illumina

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @erinyoung

Assembles organelle genomes from genomic data

Add the following snippet to your workflow script to include this module.

include { GETORGANELLE_FROMREADS } from 'nf-core/getorganelle/fromreads'

MIT License

Process

`Name`	`GETORGANELLE_FROMREADS`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`fastq` file	Input fastq files `*.{fastq.gz}`

#2 tuple

`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)
`db` directory	GetOrganelle database

Output 3 channels

#1 etc

`results/*` file	Other output files

#2 fasta tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`results/${prefix}.${organelle_type}.fasta.gz` file	Complete or partial organelle sequences `*.fasta.gz`

#3 versions_getorganelle tuple

`${task.process}` string	The name of the process
`getorganelle_from_reads` string	The name of the tool
`get_organelle_from_reads.py --version 2>&1 \| sed -n 's/GetOrganelle //p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
getorganelle	Get organelle genomes from genome skimming data	https://github.com/Kinggerm/GetOrganelle

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:21:19 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgetorganelle%2Ffromreads/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/getorganelle/fromreads/blobs/sha256:4d7b99850a183537a5b5ea3258551d5743ac78d3ed4433d2a053d1e53e96a8af
Size	2.9 KB
Checksum	sha256:4d7b99850a183537a5b5ea3258551d5743ac78d3ed4433d2a053d1e53e96a8af
Downloads	2

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:21:19 (UTC)	2	2.9 KB
0.0.0-3fc6d40	22 Apr 2026 15:13:53 (UTC)	3	2.9 KB
0.0.0-0c7146d	08 Apr 2026 19:05:58 (UTC)	3	2.8 KB