manifest {
  name = 'annotate/singler'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
  version = 'processing-workflows-quantile-filtering'
  description = 'SingleR performs reference-based cell type annotation for single-cell RNA-seq data \nby computing Spearman correlations between test cells and reference samples with known labels, \nusing marker genes to assign the most similar cell type label to each new cell.\n'
  author = 'Dorien Roosen, Weiwei Schultz'
}

process.container = 'nextflow/bash:latest'

// detect tempdir
tempDir = java.nio.file.Paths.get(
  System.getenv('NXF_TEMP') ?:
    System.getenv('VIASH_TEMP') ?: 
    System.getenv('TEMPDIR') ?: 
    System.getenv('TMPDIR') ?: 
    '/tmp'
).toAbsolutePath()

profiles {
  no_publish {
    process {
      withName: '.*' {
        publishDir = [
          enabled: false
        ]
      }
    }
  }
  mount_temp {
    docker.temp            = tempDir
    podman.temp            = tempDir
    charliecloud.temp      = tempDir
  }
  docker {
    docker.enabled         = true
    // docker.userEmulation   = true
    singularity.enabled    = false
    podman.enabled         = false
    shifter.enabled        = false
    charliecloud.enabled   = false
  }
  singularity {
    singularity.enabled    = true
    singularity.autoMounts = true
    docker.enabled         = false
    podman.enabled         = false
    shifter.enabled        = false
    charliecloud.enabled   = false
  }
  podman {
    podman.enabled         = true
    docker.enabled         = false
    singularity.enabled    = false
    shifter.enabled        = false
    charliecloud.enabled   = false
  }
  shifter {
    shifter.enabled        = true
    docker.enabled         = false
    singularity.enabled    = false
    podman.enabled         = false
    charliecloud.enabled   = false
  }
  charliecloud {
    charliecloud.enabled   = true
    docker.enabled         = false
    singularity.enabled    = false
    podman.enabled         = false
    shifter.enabled        = false
  }
}

process{
  withLabel: mem1gb { memory = 1000000000.B }
  withLabel: mem2gb { memory = 2000000000.B }
  withLabel: mem5gb { memory = 5000000000.B }
  withLabel: mem10gb { memory = 10000000000.B }
  withLabel: mem20gb { memory = 20000000000.B }
  withLabel: mem50gb { memory = 50000000000.B }
  withLabel: mem100gb { memory = 100000000000.B }
  withLabel: mem200gb { memory = 200000000000.B }
  withLabel: mem500gb { memory = 500000000000.B }
  withLabel: mem1tb { memory = 1000000000000.B }
  withLabel: mem2tb { memory = 2000000000000.B }
  withLabel: mem5tb { memory = 5000000000000.B }
  withLabel: mem10tb { memory = 10000000000000.B }
  withLabel: mem20tb { memory = 20000000000000.B }
  withLabel: mem50tb { memory = 50000000000000.B }
  withLabel: mem100tb { memory = 100000000000000.B }
  withLabel: mem200tb { memory = 200000000000000.B }
  withLabel: mem500tb { memory = 500000000000000.B }
  withLabel: mem1gib { memory = 1073741824.B }
  withLabel: mem2gib { memory = 2147483648.B }
  withLabel: mem4gib { memory = 4294967296.B }
  withLabel: mem8gib { memory = 8589934592.B }
  withLabel: mem16gib { memory = 17179869184.B }
  withLabel: mem32gib { memory = 34359738368.B }
  withLabel: mem64gib { memory = 68719476736.B }
  withLabel: mem128gib { memory = 137438953472.B }
  withLabel: mem256gib { memory = 274877906944.B }
  withLabel: mem512gib { memory = 549755813888.B }
  withLabel: mem1tib { memory = 1099511627776.B }
  withLabel: mem2tib { memory = 2199023255552.B }
  withLabel: mem4tib { memory = 4398046511104.B }
  withLabel: mem8tib { memory = 8796093022208.B }
  withLabel: mem16tib { memory = 17592186044416.B }
  withLabel: mem32tib { memory = 35184372088832.B }
  withLabel: mem64tib { memory = 70368744177664.B }
  withLabel: mem128tib { memory = 140737488355328.B }
  withLabel: mem256tib { memory = 281474976710656.B }
  withLabel: mem512tib { memory = 562949953421312.B }
  withLabel: cpu1 { cpus = 1 }
  withLabel: cpu2 { cpus = 2 }
  withLabel: cpu5 { cpus = 5 }
  withLabel: cpu10 { cpus = 10 }
  withLabel: cpu20 { cpus = 20 }
  withLabel: cpu50 { cpus = 50 }
  withLabel: cpu100 { cpus = 100 }
  withLabel: cpu200 { cpus = 200 }
  withLabel: cpu500 { cpus = 500 }
  withLabel: cpu1000 { cpus = 1000 }
}

includeConfig("nextflow_labels.config")
