This repository hosts a pipeline for analysing shotgun metagenomic data. The pipeline is developed with Nextflow and is executed using Singularity containers.
The pipeline is intended to be executed on a cluster or server. The pipeline provides configuration for a PBSPro cluster. A job submission script for running the pipeline on a PBSPro cluster is available. The command for running the pipeline is:
nextflow run metagen.nf
Options:
-c [REQUIRED] path to the configuration file
-profile [REQUIRED] server or cluster. If running on a cluster enter cluster. If running on a server enter server
--reads [REQUIRED] Path to the input raw reads. Ensure that the path is encapsulated in double quotes ("")
--blast_db [REQUIRED] Full path to the BLAST database
--deepARG [REQUIRED] Full path to the deepARG database
--quastref [REQUIRED] Full path to the reference file
--outdir [OPTIONAL] directory where pipeline will write all output file, default name is "results"
Nextflow version 21 or higher
Singularity version 3.5 or higher
The pipeline takes raw paired-end reads in fastq or fasta format.
A directory named , unless otherwise specified, will be generated in the current working directory. Notable output are:
BLAST tables
deepARG tables
Gene annotation files
Binning statistics reports
Software algorithms are available through Singularity containers. Definition files specify how the containers were developed and dependencies for each algorithm.