Description

Build ganon database using custom reference sequences.

Input

name:type
description
pattern

meta:map

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

]

input:file

List of input FASTA files, or a directory containing input FASTA files. Note you must supply —input-extension via ext.args if FASTA extensions do not end in the default fna.gz.

*

input_type:string

Specify whether the file(s) given to the input channel are in FASTA format (and will be supplied as —input) or in TSV format (and will be supplied as —input-file). For TSV format, the ‘file’ column should be just the file name so that it’s local to the working directory of this process.

fasta|tsv

taxonomy_files:file

Pre-downloaded taxonomy files of input sequences. See ganon docs for formats

genome_size_files:file

Pre-downloaded NCBI or GTDB genome size files of input sequences. See ganon docs for formats

{species_genome_size.txt.gz,*_metadata.tar.gz}

Output

name:type
description
pattern

db

meta:map

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

]

*.{hibf,ibf,tax}:file

ganon database files

*.{ibf,tax}

info

meta:map

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

]

*.info.tsv:file

Copy of target info generated. Can be used for updating database.

*info.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

ganon
MIT

ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently

github.com/pirovc/ganon 10.1093/bioinformatics/btaa458
maintainer
Github user jfy133
get in touch
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