Nextflow - Docker pipeline

Overview

This is a pipeline overview containing various tools in an easy install free nextflow environment
you dont need to install any tools with the exeption of docker and nextflow

brief tool overview

abricate -> resistance detection (via fasta or fastq files)
centrifuge -> taxonomic classification of nanopore reads (fastq)
gtdbtk -> evaluation of bins (dir input)
guppygpu -> gpu basecalling via guppy of fast5 files (dir input)
metamaps -> taxonomic classification of nanopore reads (fastq)
nanoplot -> QC of nanopore reads (fastq)
plasflow -> Plasmid prediction of assembly (fasta)
sourclass -> Determines the species of a assembly via sourmash (fasta)
sourcluster -> kmer based tree/clustering of contigs (fasta) or multiple assmeblies (via dir/)
sourmeta -> metagenomic WIMP determination via sourmash
deepHumanPathogen -> maps illumina reads against human to remove "human reads" (fastqPairs)
(and more)

Installation

intended for linux systems

Docker

install docker via sudo apt install docker.io
- or docker-ce via this
add the docker group to your user via sudo usermod -a -G docker $USER
reboot after this

Nextflow

install java runtime on your system
install nextflow via curl -s https://get.nextflow.io | bash

Usage

nextflow run replikation/docker_pipelines --help

update docker pipelines via

nextflow pull replikation/docker_pipelines

Citation

Christian Brandt. (2020, September 15). Docker pipelines: a collection of nextflow workflows related to nanopore data, taxonomy and antibiotic resistance (Version v.1.0.0). Zenodo. http://doi.org/10.5281/zenodo.4030719