ReadbasedAnalysis_cromwell.conf

# This is an example of how you can use Docker only workflows as a Cromwell
# backend provider. *This is not a complete configuration file!* The
# content here should be copy pasted into the backend -> providers section
# of the cromwell.examples.conf in the root of the repository. You should
# uncomment lines that you want to define, and read carefully to customize
# the file. If you have any questions, please open an issue at
# https://www.github.com/broadinstitute/cromwell/issues

# Documentation
# This backend doesn't have an official page, but you can read about general
# Docker use here: https://cromwell.readthedocs.io/en/develop/tutorials/Containers/#docker
# If you want to use containers, the other sections on that page will be useful to you.

backend {
  default = "Local"

  providers {

    # Example backend that _only_ runs workflows that specify docker for every command.
    Local {
      config {
        run-in-background = true
        runtime-attributes = """
          String? docker
          String? docker_user = "$EUID" 
        """
        
        submit = "/bin/bash ${script}"
        #--volume ${cwd}:${docker_cwd} \
        submit-docker = """
          shifter --image=docker:${docker} ${job_shell} ${docker_script}
        """

        dockerRoot = /global/cfs/projectdirs/m3408/aim2/metagenome/ReadbasedAnalysis/cromwell-executions
        filesystems {
          local {
            localization: [
              "hard-link", "soft-link", "copy"
            ]
            caching {
              duplication-strategy: [
                "hard-link", "soft-link", "copy"
              ]
            }
          }
        }    
     
      }
    }
  }
}

docker {
  hash-lookup {
    enabled = false
    # Set this to match your available quota against the Google Container Engine API
    #gcr-api-queries-per-100-seconds = 1000

    # Time in minutes before an entry expires from the docker hashes cache and needs to be fetched again
    #cache-entry-ttl = "20 minutes"

    # Maximum number of elements to be kept in the cache. If the limit is reached, old elements will be removed from the cache
    #cache-size = 200

    # How should docker hashes be looked up. Possible values are "local" and "remote"
    # "local": Lookup hashes on the local docker daemon using the cli
    # "remote": Lookup hashes on docker hub and gcr
    method = "local"
  }
}