Classifies metagenomic sequence data
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
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
If true mapped fastq files are saved
report
*report.txt
File containing a classification summary
*.{report.txt}
results
*results.txt
File containing classification results
*.{results.txt}
sam
*.{sam,tab}
Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s
fastq_mapped
*.mapped.fastq{,.1,.2}.gz
Mapped fastq files
*.mapped.fastq.gz
fastq_unmapped
*.unmapped.fastq{,.1,.2}.gz
Unmapped fastq files
*.unmapped.fastq.gz
versions_centrifuge
${task.process}
:string
The name of the process
centrifuge
The name of the tool
centrifuge --version 2>&1 | sed '1!d;s/.* version //'
:eval
The expression to obtain the version of the tool
versions
Centrifuge is a classifier for metagenomic sequences.
