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You can submit a Cufflinks job in batch mode with the following command:

sbatch [Slurm options] --wrap="Cufflinks [cufflinks options]"

Here you need to replace [cufflinks options] with Cufflinks command line options (please run cufflinks -h for getting a list of all command line options) and [Slurm options] with Slurm parameters for the resource requirements of the job. Please find a documentation about the parameters of sbatch on the wiki page about the batch system.