2. Running VAPER

Installing Dependencies

1. Install Nextflow

VAPER is written in Nextflow. You can find instructions about how to install Nextflow here.

2. Install a container engine

VAPER requires a container engine like Docker, Podman, or Apptainer (previously Singularity).

Note

VAPER does not currently support Conda. If you must use Conda, submit a feature request and we can work on getting this set up.

Running VAPER

Step 1. Prepare your samplesheet

VAPER requires the following information to run:

1. Sample name
2. Full path to a .gz compressed forward, Illumina read
3. Full path to a .gz compressed reverse, Illumina read

You can optionally specify reference(s) you would like to use for each sample using a semicolon-separated list of either full paths to the .gz compressed reference file(s) or the names of the reference(s) in the reference set sheet. The samplesheet below shows the following examples:

1. sample01 - required files (sample, fastq_1, fastq_2) with no references specified (reference column can be omitted)
2. sample02 - required files with references specified using file paths
3. sample03 - required files with references specified using the names of the references as supplied in the reference set sheet

samplesheet.csv:

sample,fastq_1,fastq_2,reference
sample01,/home/reads/sample01_R1.fastq.gz,/home/reads/sample01_R2.fastq.gz,
sample02,/home/reads/sample02_R2.fastq.gz,/home/reads/sample02_R2.fastq.gz,/home/refs/Mumps-1.fa.gz;/home/refs/Measles-1.fa.gz
sample03,/home/reads/sample03_R2.fastq.gz,/home/reads/sample03_R2.fastq.gz,Mumps-1;Measles-1

Step 2. Run VAPER

Below is a basic example of how to run VAPER. You can learn more about how to customize your run Inputs page.

nextflow run DOH-JDJ0303/vaper \
    -r main \
    --input samplesheet.csv \
    --outdir results \
    --max_cpus 8 \
    --max_memory 32.GB

Tip

Nextflow allows you to a resume a run using the -resume parameter.

Step 3. Check results

All results will be saved in the location specified by --outdir. You can find a summary of your run in VAPER-summary.csv. Learn more on the pipeline Outputs page.