CLUSTard

How to run

1. Install snakemake into conda environment
2. git clone https://github.com/ac1513/CLUSTard.git
3. Create data directory (containing samples [names ending in _R1.fastq.gz or _R2.fastq.gz] and assembled reference
4. Put sample prefixes into samples.tsv (samples column) in the order that you want the final plot to be
5. Edit config.yaml file
6. To run on a cluster with slurm job scheduler using snakemake --use-conda --cluster-config cluster.json --cluster "sbatch -A {cluster.account} -p {cluster.partition} -t {cluster.time} -c {cluster.threads} --mem-per-cpu {cluster.mem}" -j 500 (running in screen with logfile -L is best!)

• (Add --config then e.g. jobid=test to change config without having to edit the whole file - esp useful with the jobid and the kraken_level steps.)
• Currently needs to be run with Snakemake version 5.6.0 or lower

Known issues