config.yaml

# Commenting out 'cluster' will force jobs to be run locally.
# '>-' is yaml syntax for splitting a string over multiple lines
cluster: >-
  python ./snakemake_profile/cluster_submit.py
  --retry-submit-interval-seconds 30,120,300
  --resource-usage-dir ./snakemake_profile/job_resource_usage
cluster-status: >-
  python ./snakemake_profile/cluster_status.py
  --retry-status-interval-seconds 30,120,300
  --resource-usage-dir ./snakemake_profile/job_resource_usage
  --resource-usage-min-interval 300

# 'jobs' has two interpretations:
#  * if running with 'cluster'
#    + max number of jobs concurrently submitted to the cluster
#  * else
#    + max number of local cores to use
jobs: 100

# 'resources' defines limits that apply to both local and 'cluster' jobs.
# 'resources' is commented out when using 'cluster' to allow the cluster
# scheduler to determine the available memory.
# resources:
#   - 'mem_mb=16384'

# wait up to a minute for result files to be visible through the shared filesystem
latency-wait: 60

# Allow a failed job to be re-started once
restart-times: 1

# output settings
verbose: false
printshellcmds: true
show-failed-logs: false
reason: true