config.yaml

# Default options for running PCMP_ITS_pipeline with slurm
rerun-incomplete: True
rerun-triggers: "mtime"
latency-wait: 90
jobs: 100
keep-going: True
notemp: True
printshellcmds: True
nolock: True
verbose: True
cores: 24 # 'all' uses all available cores, you can also specify a number
cluster: "sbatch \
          --account={resources.account} \
          --partition={resources.partition} \
          --mem={resources.mem_mb} \
          --cpus-per-task={threads} \
          --time={resources.runtime} \
          --job-name={rule} \
          --output=slurm_%x_%j.out"

# Default resource configuration
default-resources:
  - account="hpcusers"
  - partition="defq"
  - runtime=120
  - mem_mb=4000
  - disk_mb=1000
# set-threads: map rule names to threads
set-threads:
  - blastn=8
  - cluster=8
  - ref_chimera=8
  - map_back=8
  - trim_r=8
  - trim_f=8
# set-resources: map rule names to resources in general
set-resources:
  - run_dnabc:mem_mb=8000
  - run_dnabc:runtime=480
  - trim_r:mem_mb=32000
  - trim_r:runtime=720
  - trim_f:mem_mb=32000
  - trim_f:runtime=720
  - cluster:mem_mb=16000
  - cluster:runtime=480
  - ref_chimera:mem_mb=8000
  - ref_chimera:runtime=720
  - map_back:mem_mb=8000
  - map_back:runtime=720
  - blastn:mem_mb=24000
  - blastn:runtime=720
  - brocc:mem_mb=24000
  - brocc:runtime=720
  - fq2fa_r:mem_mb=24000
  - fq2fa_r:runtime=720
  - get_trimmings:mem_mb=24000
  - get_trimmings:runtime=720
  - count_trimmings:mem_mb=24000
  - count_trimmings:runtime=720

configfile: "/mnt/isilon/microbiome/analysis/danielsg/PCMP_ITS_pipeline/project_config.yml"