Quick Start

Viralgenie needs two things:

1. Nextflow
2. Docker or Singularity or Conda

# Install nextflow with conda
conda install nextflow

Run the pipeline with a small test dataset with docker containers:

nextflow run Joon-Klaps/viralgenie \
    -profile test,docker

For a more complete guide on how to set up Nextflow, Docker, Singularity, and Conda, see the installation guide.

Running viralgenie with your own samples

nextflow run Joon-Klaps/viralgenie \
    -profile docker \
    --input my_samplesheet.csv

An input file contains the paths to the fastq files and the sample names. The input file can be in TSV, CSV, YAML, or JSON format.

TSVCSVYAMLJSON

input-samplesheet.tsv

sample  fastq_1 fastq_2
sample1 AEG588A1_S1_L002_R1_001.fastq.gz    AEG588A1_S1_L002_R2_001.fastq.gz
sample2 AEG588A5_S5_L003_R1_001.fastq.gz
sample3 AEG588A3_S3_L002_R1_001.fastq.gz    AEG588A3_S3_L002_R2_001.fastq.gz

input-samplesheet.csv

sample,fastq_1,fastq_2
sample1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
sample2,AEG588A5_S5_L003_R1_001.fastq.gz,
sample3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz

input-samplesheet.yaml

- sample: sample1
fastq1: AEG588A1_S1_L002_R1_001.fastq.gz
fastq2: AEG588A1_S1_L002_R2_001.fastq.gz
- sample: sample2
fastq1: AEG588A5_S5_L003_R1_001.fastq.gz
- sample: sample3
fastq1: AEG588A3_S3_L002_R1_001.fastq.gz
fastq2: AEG588A3_S3_L002_R2_001.fastq.gz

samplesheet.json

[
    {
        "sample": "sample1",
        "fastq1": "AEG588A1_S1_L002_R1_001.fastq.gz",
        "fastq2": "AEG588A1_S1_L002_R2_001.fastq.gz",
    },
    {
        "sample": "sample2",
        "fastq1": "AEG588A5_S5_L003_R1_001.fastq.gz",
    },
    {
        "sample": "sample3",
        "fastq1": "AEG588A3_S3_L002_R1_001.fastq.gz",
        "fastq2": "AEG588A3_S3_L002_R2_001.fastq.gz",
    }
]