nextflow.config

// Execution environment for miscellaneous tasks
params.roadie = 'ghcr.io/labsyspharm/mcmicro:roadie-2023-10-25'

// The mode for transfering output between work and project directories
params.publish_dir_mode = 'copy'

// Platform-specific profiles
profiles {

  /****************************
  * Platform-specific configs *
  ****************************/

  // Default profile, best suited for local runs
  standard {
    includeConfig 'config/nf/docker.config'
  }

  // Profile for using singularity to run module containers
  singularity {
    includeConfig 'config/nf/singularity.config'
  }

  // Profile specific to the HMS compute cluster
  O2 {
    includeConfig 'config/nf/O2base.config'
    singularity.cacheDir  = '/n/groups/lsp/mcmicro/singularity'
  }

  // Same as O2, but for external users not in the `lsp` group
  O2ext {
    includeConfig 'config/nf/O2base.config'
    singularity.cacheDir = "$HOME/.mcmicro"
  }

  // Amazon Web Services
  AWS {
    includeConfig 'config/nf/aws.config'
  }
  
  // Nextflow tower
  tower {
    includeConfig 'config/nf/tower.config'
  }

  /****************************
  * Resource-specific configs *
  ****************************/

  WSI {
    includeConfig 'config/nf/wsi.config'
  }

  TMA {
    includeConfig 'config/nf/tma.config'
  }

  GPU {
    docker.runOptions = '--cpus 0.000 -u root --entrypoint "" --gpus all'
    singularity.runOptions = '-C -H "$PWD" --nv'
    
    process{
      withName: 'segmentation:worker' {
        queue = 'gpu'
        clusterOptions = '--gres=gpu:1'
      }
    }
  }

  /**************************
  * Backwards compatibility *
  **************************/
  
  // Profiles below this line are deprecated
  // Left here for backwards compatibility

  // Same as -profile O2,WSI
  O2WSI {
    includeConfig 'config/nf/O2base.config'
    includeConfig 'config/nf/wsi.config'
  }

  // Same as -profile O2,TMA
  O2TMA {
    includeConfig 'config/nf/O2base.config'
    includeConfig 'config/nf/tma.config'
  }

  // Same as -profile O2,WSI
  O2massive {
    includeConfig 'config/nf/O2base.config'
    includeConfig 'config/nf/wsi.config'
  }

}