Description

Download a mitochondrial genome to be used as reference for MitoHiFi.

NOTE: An optional NCBI API key can be supplied to MITOHIFI_FINDMITOREFERENCE. This should be set using Nextflow’s secrets functionality:

nextflow secrets set NCBI_API_KEY <key>

See https://www.nextflow.io/docs/latest/secrets.html for more information.

Input

name:type
description
pattern

meta:map

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

species:string

Latin name of the species for which a mitochondrial genome should be fetched

[A-Z]?[a-z]* [a-z]*

Output

name:type
description
pattern

fasta

meta:map

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

*.fasta:file

Downloaded mitochondrial genome in Fasta format

*.{fasta,fa}

gb

meta:map

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

*.gb:file

Downloaded mitochondrial genome in Genbank format

*.gb

versions

versions.yml:file

File containing software versions

versions.yml

Tools

findMitoReference.py
MIT

Fetch mitochondrial genome in Fasta and Genbank format from NCBI

github.com/marcelauliano/MitoHiFi 10.1101/2022.12.23.521667
maintainer
Github user verku
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