PBS/Torque batch scheduler profile

Snakemake profile for the submission of scripts trhough the PBS/Torque batch scheduler (qsub command).

PBS/Torque

qsub

Schedulers

Table of contents

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Snakemake provides the ability to declare resource declarations for a wide array of bach scheduler resources such as RAM or CPUs.

The provided batch scheduler profile was created from a template provided by snakemake. It has however been altered to facilitate declaring batch scheduler resource usage on a per-rule basis.

Parallelization warning

The ability to set granular resource allocations per-rule was required to achieve parallel rule execution. As such, this pipeline contains rule syntax that is non-standard, to facilitate this paralelization.

Finding ways to standardize this for scalability have been noted and will be investigated when resources allow.