manifest {
  name = 'bedtools/bedtools_split'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
  version = 'main'
  description = 'Split a BED file into multiple output files using different algorithms.\n\nbedtools split divides a single BED file into multiple smaller BED files \nbased on the specified number of output files and splitting algorithm. This \nis useful for parallelizing analysis workflows, creating balanced datasets, \nor distributing genomic intervals across multiple processing units.\n\nThis tool is commonly used for:\n- Parallelizing genomic analysis workflows by splitting input data\n- Creating balanced datasets for distributed computing\n- Dividing large BED files for memory-efficient processing\n- Preparing input files for parallel execution frameworks\n- Load balancing genomic intervals across multiple processes\n- Creating subsets of genomic data for testing or validation\n'
  author = 'Robrecht Cannoodt'
}

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 }
}


