manifest {
  name = 'bedtools/bedtools_multiinter'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
  version = 'main'
  description = 'Identify common intervals among multiple BED/GFF/VCF files.\n\nbedtools multiinter finds regions that are shared across multiple interval files and \nreports statistics about the overlaps. It can identify intervals that are present in \nall files, some files, or generate a matrix showing which intervals are found in which files.\n\nThis tool is commonly used for:\n- Finding consensus regions across multiple datasets\n- Identifying tissue-specific or condition-specific intervals\n- Creating intersection matrices for comparative analysis\n- Merging annotations from multiple sources\n- Quality control of peak calling across replicates\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 }
}


