Classifies metagenomic sequence data
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
report
*report.txt:file
File containing a classification summary
*.{report.txt}
results
*results.txt:file
File containing classification results
*.{results.txt}
sam
*.{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
*.mapped.fastq{,.1,.2}.gz:file
Mapped fastq files
*.mapped.fastq.gz
fastq_unmapped
*.unmapped.fastq{,.1,.2}.gz:file
Unmapped fastq files
*.unmapped.fastq.gz
versions
versions.yml:file
File containing software versions
versions.yml
Centrifuge is a classifier for metagenomic sequences.
