nextflow.config

nextflowVersion = '>=20'

manifest {
    homePage = 'https://gitbio.ens-lyon.fr/LBMC/nextflow'
    description = 'pipeline to '
    mainScript = 'main.nf'
    version = '0.0.0'
}

report {
  enabled = true
  file = "$baseDir/../results/report.html"
}

profiles {
  docker {
    docker.temp = "auto"
    docker.enabled = true
    process {
      errorStrategy = 'finish'
      memory = '16GB'
      withLabel: big_mem_mono_cpus {
        cpus = 1
      }
      withLabel: big_mem_multi_cpus {
        cpus = 4
      }
      withLabel: small_mem_mono_cpus {
        cpus = 1
        memory = '2GB'
      }
      withLabel: small_mem_multi_cpus {
        cpus = 4
        memory = '2GB'
      }
    }
  }
  podman {
    podman.enabled = true
    process {
      errorStrategy = 'finish'
      memory = '16GB'
      withLabel: big_mem_mono_cpus {
        cpus = 1
      }
      withLabel: big_mem_multi_cpus {
        cpus = 4
      }
      withLabel: small_mem_mono_cpus {
        cpus = 1
        memory = '2GB'
      }
      withLabel: small_mem_multi_cpus {
        cpus = 4
        memory = '2GB'
      }
    }
  }
  singularity {
    singularity.enabled = true
    singularity.cacheDir = "./bin/"
    process {
      errorStrategy = 'finish'
      memory = '16GB'
      withLabel: big_mem_mono_cpus {
        cpus = 1
      }
      withLabel: big_mem_multi_cpus {
        cpus = 4
      }
      withLabel: small_mem_mono_cpus {
        cpus = 1
        memory = '2GB'
      }
      withLabel: small_mem_multi_cpus {
        cpus = 4
        memory = '2GB'
      }
    }
  }
  psmn {
    singularity.enabled = true
    singularity.cacheDir = "/Xnfs/abc/singularity/"
    singularity.runOptions = "--bind /Xnfs,/scratch"
    process{
      errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
      maxRetries = 3
      withLabel: big_mem_mono_cpus {
        executor = "sge"
        clusterOptions = "-cwd -V"
        cpus = 1
        memory = "128GB"
        time = "12h"
        queue = "monointeldeb128,monointeldeb192"
      }
      withLabel: big_mem_multi_cpus {
        executor = "sge"
        clusterOptions = "-cwd -V"
        cpus = 32
        memory = "192GB"
        time = "24h"
        queue = "CLG*,SLG*,Epyc*"
        penv = "openmp32"

      }
      withLabel: small_mem_mono_cpus {
        executor = "sge"
        clusterOptions = "-cwd -V"
        cpus = 1
        memory = "16GB"
        time = "12h"
        queue = "monointeldeb128,monointeldeb192"
      }
      withLabel: small_mem_multi_cpus {
        executor = "sge"
        clusterOptions = "-cwd -V"
        cpus = 32
        memory = "16GB"
        time = "24h"
        queue = "CLG*,SLG*,Epyc*"
        penv = "openmp32"

      }
    }
  }
  ccin2p3 {
    singularity.enabled = true
    singularity.cacheDir = "$baseDir/.singularity_in2p3/"
    singularity.runOptions = "--bind /pbs,/sps,/scratch"
    process{
      errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
      maxRetries = 3
      withLabel: big_mem_mono_cpus {
        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"
        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
        cpus = 1
        memory = "8GB"
        queue = "huge"
      }
      withLabel: big_mem_multi_cpus {
        container = "lbmc/urqt:d62c1f8"
        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"
        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
        cpus = 1
        memory = "8GB"
        queue = "huge"
      }
      withLabel: small_mem_mono_cpus {
        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"
        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
        cpus = 1
        memory = "8GB"
        queue = "huge"
      }
      withLabel: small_mem_multi_cpus {
        container = "lbmc/urqt:d62c1f8"
        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"
        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
        cpus = 1
        memory = "8GB"
        queue = "huge"
      }
    }
  }
}