bam_to_bigwig.config 2.18 KB
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profiles {
  docker {
    docker.temp = 'auto'
    docker.enabled = true
    process {
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      withName: index_bam {
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        container = "lbmc/sambamba:0.6.7"
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        cpus = 4
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      }
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      withName: bam_to_bigwig {
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        container = "lbmc/deeptools:3.0.2"
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        cpus = 4
      }
    }
  }
  singularity {
    singularity.enabled = true
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    singularity.cacheDir = "./bin/"
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    process {
      withName: index_bam {
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        container = "lbmc/sambamba:0.6.7"
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        cpus = 4
      }
      withName: bam_to_bigwig {
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        container = "lbmc/deeptools:3.0.2"
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        cpus = 4
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      }
    }
  }
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  psmn{
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    process{
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      withName: index_bam {
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        beforeScript = "source $baseDir/.conda_psmn.sh"
        conda = "$baseDir/.conda_envs/sambamba_0.6.7"
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        executor = "sge"
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        clusterOptions = "-cwd -V"
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        cpus = 16
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        memory = "30GB"
        time = "24h"
        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
        penv = 'openmp16'
      }
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      withName: bam_to_bigwig {
        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
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        module = "deeptools/3.0.2"
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        executor = "sge"
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        clusterOptions = "-cwd -V"
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        cpus = 16
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        memory = "30GB"
        time = "24h"
        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
        penv = 'openmp16'
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      }
    }
  }
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  ccin2p3 {
    singularity.enabled = true
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    singularity.cacheDir = "$baseDir/.singularity_in2p3/"
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    singularity.runOptions = "--bind /pbs,/sps,/scratch"
    process{
      withName: index_bam {
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        container = "lbmc/sambamba:0.6.7"
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        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"
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        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
        "
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        cpus = 1
        queue = 'huge'
      }
      withName: bam_to_bigwig {
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        container = "lbmc/deeptools:3.0.2"
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        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"
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        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
        "
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        cpus = 1
        queue = 'huge'
      }
    }
  }
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}