Description

Classifies metagenomic sequence data

Input

name:type
description
pattern

meta:map

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

]

reads:file

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

db:directory

Path to directory containing centrifuge database files

save_unaligned:boolean

If true unmapped fastq files are saved

save_aligned:boolean

If true mapped fastq files are saved

Output

name:type
description
pattern

report

meta:map

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

]

*report.txt:file

File containing a classification summary

*.{report.txt}

results

meta:map

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

]

*results.txt:file

File containing classification results

*.{results.txt}

sam

meta:map

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

]

*.{sam,tab}:file

Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s

*.{sam,tab}

fastq_mapped

meta:map

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

]

*.mapped.fastq{,.1,.2}.gz:file

Mapped fastq files

*.mapped.fastq.gz

fastq_unmapped

meta:map

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

]

*.unmapped.fastq{,.1,.2}.gz:file

Unmapped fastq files

*.unmapped.fastq.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

centrifuge
GPL v3

Centrifuge is a classifier for metagenomic sequences.