nextflow.config

process {
    withName: image_to_zarr {
        memory = 40.GB
        cpus = 4
    }

    withName: ome_zarr_metadata {
        memory = 2.GB
        cpus = 1
    }

    withName: route_file {
        // max between 4GB or size of sparce matrix
        memory = 64.GB
        cpus = 1
    }

    withName: Build_config {
        memory = 2.GB
        cpus = 1
    }

    withName: Generate_image {
        memory = 40.GB
        cpus = 4
    }
}

profiles {

  conda {
    conda.enabled = true
    process {
      conda = "$projectDir/envs/environment.yaml"
      withLabel: build_config {
        conda = "$projectDir/envs/build_config/environment.yaml"
      }
    }
  }

  docker {
    docker.enabled = true
    process {
      container = 'haniffalab/webatlas-pipeline:0.5.3'
      withLabel: build_config {
        container = 'haniffalab/webatlas-pipeline-build-config:0.5.2'
      }
    }
  }

  singularity {
    singularity.enabled = true
    singularity.autoMounts = true
    process {
      container = 'haniffalab/webatlas-pipeline:0.5.3'
      withLabel: build_config {
        container = 'haniffalab/webatlas-pipeline-build-config:0.5.3'
      }
    }
  }

  sanger {
    executor {
        name = 'lsf'
        perJobMemLimit = true
    }

    process.executor = 'lsf'
    process.queue = 'normal'
    singularity.runOptions  = '--bind $(mktemp -d /tmp/webatlas.XXXXX):/tmp --env NUMBA_CACHE_DIR=/tmp'
  }
}