Can use helper script pipe.sub for pipeline job submission.
Start by activating miniconda
source ~/Miniconda/bin/activate
Create conda environment with Snakemake and pipeline global dependencies defined in environment.yaml.
conda env create -n ont-ul-pipe
After creating the pipeline environment, activate the environment using conda activate ont-ul-pipe
Run pipeline using a command similar to the one below, code after --cluster-config only for running on a cluster, pipe.sub is a helper script for pipeline job submission.
snakemake --use-conda -j 999 --cluster-config cluster.json \
--cluster "sbatch -J {cluster.name} \
-p {cluster.partition} \
-n {cluster.n} \
--mem {cluster.mem} \
-t {cluster.time} \
{cluster.resources} \
-e {cluster.error} \
-o {cluster.output} \
--mail-type ALL \
--profile ALL"