Quick Start

VAPER requires Nextflow and one of the following container engines: Docker, Podman, Apptainer, Singularity.

1. Make your samplesheet:

Samplesheets must use absolute file paths to avoid path resolution errors.

samplesheet.csv:

sample,fastq_1,fastq_2
sample1,sample1_R1.fastq.gz,sample1_R2.fastq.gz
sample2,sample2_R1.fastq.gz,sample2_R2.fastq.gz

2. Run VAPER:

This uses the default reference set, which includes [loading] viral taxa (full list). It is also possible to supply your own reference(s) in the samplesheet or via the --refs parameter (learn more).

nextflow run doh-jdj0303/vaper \
    -r main \
    -profile docker \
    --input $PWD/samplesheet.csv \
    --db $PWD/db \
    --outdir $PWD/results \
    --max_cpus 4 \
    --max_memory 8.GB

3. Check the results:

Results can be found in --outdir. A good place to start is VAPER-summary.csv. Genome assemblies can be found in ${outdir}/${sample}/assembly/ and metagenomic summary in ${outdir}/${sample}/metagenome (learn more).

🔍 Want to learn more? Check out the getting started and overview pages.