Difference between revisions of "Using Snakemake on the HPC Cluster"

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(Created initial coding example for snakemake)
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Revision as of 19:50, 16 May 2024

Setup

executor: slurm
jobs: 100

default-resources:
    mem_mb: max(1.5 * input.size_mb, 100)
    account: <ACCOUNT_NAME>
    partition: <PARTITION NAME>
set-threads:
    myrule: max(input.size_mb / 5, 2)
set-resources:
    myrule:
        mem_mb: attempt * 200
  • Create a Snakefile (see
    • You can over-ride resources with that flag otherwise it will use the values in testprofile
  • Run the Snakefile with this command
    snakemake --profile testprofile  -j 1 --executor cluster-generic --cluster-generic-submit-cmd "batch" ...