cluster_config.yaml

__default__:
  system: "pbs"

# default parameter for all rules
# for steps, where memory/threads are not specified in the Snakefilecan

  # `time`, `mem` defaults could be overridden from `resources:` section
  time:    "20" # minutes
  mem:     "4"  # GB

  # `threads` defaults could be overridden by `threads`
  threads: 1

  #account: ""
  #queue: "{{cookiecutter.default_queue}}" # auto-detection in our case
  nodes: 1
  merge_std: "oe"
  log: "{log}"
  # name: "{rule}"
  sampleid: ""

# Comma separated options keys list from rule 'params' section which could override default option
# values
  rule_params_options: "sampleid"

# only parameters defined in key_mapping (see below) are passed to the command in the order specified.

  # Example

  #PBS -N fastq-dump_${WORK_DIR_NAME}_${FILE_NAME_WO_EXT}
  #PBS -l nodes=1:ppn=4,walltime=24:00:00,vmem=32gb
  #PBS -j oe
  #PBS -o ${OUTDIR}/${FILE_NAME_WO_EXT}_fastq_dump.log

  command_options:
    pbs:
      command: "qsub"
      key_mapping:
        name: " -N sj{jobid}{sampleid}.{name}.{pid}"
        # account: " -W group_list={account}"
        # queue: " -q {queue}"

        nodes: " -l nodes={nodes}" # -l has to be on first resource element
        threads: ":ppn={threads},"
        mem: "vmem={mem}gb,"
        mem_ram: "mem={mem_ram}gb,"
        time: "walltime={time}:00" #[[HH:]MM:]SS


        merge_std: " -j {merge_std}" # merge stdout, stderr
        log: " -o {log}_job.log"


# specific parameters for certain rules, which need more time/memory

#run_assembler:
#  queue: bigmem
#  time: 1710
#   threads and memory defined in config file