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nf-LO

nf-LO is a nextflow pipeline to generate liftOver chain/net files for any pair of genomes and to optionally perform the lift over.

Install

See here for instructions on how to install the software and/or its dependencies.

The workflow

The workflow consists of four major steps:

1. Chunking of the genomes: not always needed, but can speed up the work!
2. Alignment: this step can be performed using different aligners; fine tuning it can greatly improve the results.
3. Chain/netting: generation of the chain/net for the liftover.
4. Lift the positions: if a file is specified, it will be automatically lifted (if possible).

If you have a couple of genomes that you want to process, you can simply follow our step-by-step guide, which will get you up and running with nf-LO!

If you want more control over the workflow, and want to try and improve your newly generated chain/net files, simply follow the sub-sections below:

1. Inputs
2. Alignments
3. Chain/Net
4. Liftover
5. Outputs
6. Reports

See the custom configurations section for how to run the workflow on your local system.

Resources

By default, nf-LO will attempt to use all cores but one and an amount of memory equal to the one reserved by the java virtual machine. For most cases, will have to customize these values to match the requirements to successfully run the workflow. To do so, users can specify the settings as follow:

1. --max_cpus: maximum number of cpus requested and used by the tasks (e.g. --max_cpus 4 will use at most 4 cpus for a single job)
2. --max_time: maximum time to use for a single job (e.g. --max_time 12.h will run a task for at most 12 hours)
3. --max_memory: maximum memory used by a single job (e.g. --max_memory 16.GB will use at most 16 GB of ram for a job)