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