Analysis pipeline by Forde Lab.
Bioinfomatics development by Dr. Brian Forde, coding by Thom Cuddihy
SnapperRocks requires that Nextflow v20+ be installed to run, which is compatible with Linux and OSX.
Compute environments are provided in Singularity/Apptainer containers for local and cluster deployment. For AWS deployment, instances may be created from the containers.
After pulling, you will need to download the latest published Singularity containers:
- General Container, MD5: eb324ed5ee10d303a2b2d92358565388
- Kraken2 Container, MD5: fac635cecaf4af8f28c8b01252b19900
- Nesoni Container, MD5: df1b5c1deef639ccdae05a2d66364ed1
Update the nextflow.config file as appropriate for Singularity container location (default is '/data/images/').
SnapperRocks may be launched from the command line, using the Nextflow binary and the pipeline’s main.nf file. Any changes to the default values (see User Guide) may be specified with a -- prefix and then the value. For Boolean parameters, a true value may be indicated with just the -- prefix.
Defaults may be permanently changed by editing the nextflow.config file in the path of SnapperRocks’ main.nf.
E.g.:
nextflow /path/to/SnapperRocks/main.nf --run_id "run_71" --fastq "/ftp/ingest/*_R{1,2}.fastq.gz" --trim --taxoprofile --assembly --typing --nesoni --cluster --executor "slurm"At a minimum, the values that change between runs should be specified on the command line (e.g. run_id, and depending on data ingest and handling fastq and/or results)
Parameters that will stay the same between runs may be updated in the nextflow.config or left as command line arguments and stored as a batch file for record keeping.
Example data is available for download here, MD5: 556e88b1b454d40d17e24376da2e1e43