nf-groot

A Nextflow pipeline for running Groot, which is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples.

Input samples

The input for the pipeline is a set of reads given as pairs. For example:

17.R1.fq.gz
17.R2.fq.gz
S7.350.R1.fq.gz
S7.350.R2.fq.gz
...

Running in Nextflow

Check usage:

nextflow run iamgroot.nf --help

Search for the sample reads S15_350, using the arg-annot default database (db-arg) executed in a distributed environment (check our DiGenomaLab cluster).

nextflow -bg run iamgroot.nf --reads 'reads/17.R{1,2}.fq.gz' -c nextflow.config -profile kutral

Software versions

• Groot: 1.1.2
• Nextflow: 23.04.2