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Nextflow - Docker pipeline

DOI

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