Description

Classify FASTQ files against ganon database

Input

name:type
description
pattern

meta:map

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

]

fastqs:file

Single or paired FASTQ files, optionally gzipped

*.{fq,fq.gz,fastq,fastq.gz}

db:file

Ganon database files from build or build-custom

*.{ibf,tax}

Output

name:type
description
pattern

tre

meta:map

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

]

*.tre:file

Full ganon report file

*.tre

report

meta:map

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

]

*.rep:file

Plain ganon report file with only targets with match

*.rep

one

meta:map

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

]

*.one:file

Information about a single (best) match of a given read after EM or LCA algorithms

*.one

all

meta:map

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

]

*.all:file

Information of all matches to a given read

*.all

unc

meta:map

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

]

*.unc:file

List of all reads without a hit

*.unc

log

meta:map

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

]

*.log:file

Text file containing console output from ganon classify

*.log

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