Repro_PMID_29795788

Reproducing Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

Install Docker on AWS VM

sudo apt-get update 
sudo apt-get install docker-ce
sudo groupadd docker 
sudo usermod -aG docker ubuntu 
sudo service docker restart 
Restart VM

Replication pipeline:

• Pipeline written in Snakemake (pythonic workflow language)
• Located on AWS instance at scripts/Snakefile_replication_PMID29795788
• Requirements to run:
  • Sample file (see sample_manifest)
    • Space-separated file consisting of: sample_name read1.fastq read2.fastq
  • Paths (set up in the snakefile - should probably be moved to a config file at some point):

    adapterFile = 'refs/contaminating_primers.fasta'
    sampleFile = '/home/ubuntu/sample_manifest'
    inDir = '/home/ubuntu/data/'
    dt = datetime.datetime.now().strftime('%Y%m%d%H%M%S')
    outDir = '/home/ubuntu/pipeline_' + dt + '/'
    

• To run: snakemake -s scripts/Snakefile_replication_PMID29795788 --use-singularity --cores 16
• After running, look for output in pipeline_<datetime>