Snakemake Workflows

by
Lauren Tso
Kevin Bonham, PhD Deniz Uzun

Initial setup

$ poetry install
$ conda install -c bioconda trimmomatic trf

Use poetry shell with this directory as the working directory every time you're ready to use.

bioBakery databases

$ metaphlan --install --bowtie2db $METAPHLAN_DATABASE_DIR # be sure to set this in `config.yaml` as well
$ kneaddata_database --download human_genome bowtie2 $KNEADDATA_DATABASE_DIR
$ humann_databases --download uniref uniref90_diamond $HUMANN_DATABASE_DIR
$ humann_databases --download chocophlan full $HUMANN_DATABASE_DIR
$ humann_databases --download utility_mapping full $HUMANN_DATABASE_DIR

Usage

1. Make a copy of config_template.yaml called config.yaml.
2. Make a copy of cluster_config.yaml called cluster.yaml.
3. Set the variables for your environment.
4. Run:

$ snakemake -s /home/vklepacc/software/repos/snakemake_workflows/run.smk \
    --configfile config.yaml --cluster-config cluster.yaml \
    --cluster "sbatch -n {cluster.processors} -N 1 -t {cluster.time} --mem {cluster.memory} -o output/logs/{rule}-%j.out -e output/logs/{rule}-%j.err -p newnodes" \
    --jobs 16 --latency-wait 15