1. Quick Start

Important

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

1. Make your samplesheet:

Note

The example below creates a reference set for each taxon using data automatically downloaded from NCBI. It is also possible to supply your own sequence data with or without the NCBI data - learn more here.

samplesheet.csv:

taxon,segmented,segmentSynonyms
Hantavirus,TRUE,s|small;m|medium|middle;l|large
Norovirus,FALSE,

Step 2. Run EPITOME

Run EPITOME using the command below.

nextflow run DOH-JDJ0303/epitome \
    -r main \
    -profile docker \
    --input samplesheet.csv \
    --outdir results

Tip

Want to learn more? Check out the pipeline overview here.