Nanopore assembly pipeline

This is a draft nanopore assembly pipeline used by some groups at the CCDM. More documentation to come.

Examples

nextflow run ccdmb/nanopore_assembly -resume -latest --nanoporeReads "*.fastq.gz"

Profiles

We have a few profiles available to customise how the pipeline will run.

• nimbus sets the canu assembler to use 8 CPUs and 30GB RAM.
• zeus sets the canu assembler to use 14 CPUs and 64GB RAM, and sets some cluster specific options to use the slurm based scheduler at Pawsey.
• docker and docker_sudo sets it to use docker containers, docker_sudo is identical except that docker is run as root (required for some installations of docker).
• singularity sets it to use singularity containers, these are automatically converted from docker containers.

# Using docker
nextflow run ccdmb/nanopore_assembly -profile docker -resume -latest --nanoporeReads "*.fastq.gz"

# Using docker, and also increasing CPUs for canu.
nextflow run ccdmb/nanopore_assembly -profile docker,nimbus -resume -latest --nanoporeReads "*.fastq.gz"

Parameters

--nanoporeReads <glob>
    Required
    A glob of the fastq.gz files of the adapter and barcode trimmed reads.
    The basename of the file needs to match the basename of the respective genome.

--canuSlow
    Default: false
    Disables canu fast mode.

--outdir <path>
    Default: `assembly`
    The directory to store the results in.