manifest {
  name = 'genetic_demux/demuxlet'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
  version = 'v4.0.1'
  description = 'Demuxlet is a software tool to deconvolute sample identity and identify multiplets when\nmultiple samples are pooled by barcoded single cell sequencing. If external genotyping data\nfor each sample is available (e.g. from SNP arrays), demuxlet would be recommended. Be careful\nthat the parameters on the github is not in line with the newest help version.\n'
  author = 'Xichen Wu'
}

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")
