Classifies metagenomic sequence data
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
reads
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
db
Path to directory containing centrifuge database files
save_unaligned
If true unmapped fastq files are saved
save_aligned
If true mapped fastq files are saved
report
File containing a classification summary
*.{report.txt}
results
File containing classification results
*.{results.txt}
sam
Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s
*.{sam,tab}
fastq_unmapped
Unmapped fastq files
*.unmapped.fastq.gz
fastq_mapped
Mapped fastq files
*.mapped.fastq.gz
versions
File containing software versions
versions.yml
Centrifuge is a classifier for metagenomic sequences.