Skip to content

Snakemake pipeline for processing ultra-long ONT datasets.

Notifications You must be signed in to change notification settings

nate-d-olson/giab-ont-ul-pipeline

Repository files navigation

Pipeline for processing JIMB UL ONT dataset

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"

About

Snakemake pipeline for processing ultra-long ONT datasets.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published