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