enterovirus-NF

Nextflow pipeline for de novo assembly of enterovirus genomes

Usage:

nextflow run enterovirus.nf --inputfq 'reads/*_R{1,2}_001.fastq.gz' -profile ( slurm | local )

    REQUIRED

	--inputfq [Fileglob that matches your input reads, must be surrounded with 
                    'single-quotes' prevent shell expansion]

	-profile [If you are running this on a SLURM cluster, set to 'slurm' to submit jobs to 
	          the scheduler. If not, set 'local']

    OPTIONAL

	--output [Path to output directory, 'enterovirus-NF.out' by default]

	--bbnorm_target [Kmer normalization target for bbnorm, 5000 by default]

Outputs:

Filename	File content
vapor/{SAMPLENAME}.ref.out	VAPOR statistics
vapor/{SAMPLENAME}.ref.fa	VAPOR selected reference sequence
mapping/{SAMPLENAME}.assembly_mapping.sorted.bam	Reads mapped to sample assembly
mapping/{SAMPLENAME}.reference_mapping.sorted.bam	Reads mapped to reference sequence
mapping/{SAMPLENAME}.assembly_mapping.normalized.sorted.bam	Normalized reads mapped to assembly
assembly/{SAMPLENAME}.iva.fa	Sample assembly
assembly/{SAMPLENAME}.shiver.fa	Sample assembly post-processed with Shiver

Depends:

• Nextflow (https://www.nextflow.io/)
• Conda (Install miniconda: https://docs.conda.io/en/latest/miniconda.html)
• Conda channels bioconda and conda-forge (https://bioconda.github.io/#set-up-channels)