Description

Assembles organelle genomes from genomic data

Input

name:type
description
pattern

meta:map

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

fastq:file

Input fastq files

*.{fastq.gz}

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

name:type
description
pattern

fasta

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

etc

results/*:file

Other output files

versions

versions.yml:file

File containing software versions

versions.yml

Tools

getorganelle
GPL v3

Get organelle genomes from genome skimming data

github.com/Kinggerm/GetOrganelle 10.1186/s13059-020-02154-5
maintainer
Github user erinyoung
get in touch
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