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18 results

bam_to_bigwig.config

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  • Laurent Modolo's avatar
    87c79ae2
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    bam_to_bigwig.config 1.90 KiB
    profiles {
      docker {
        docker.temp = "auto"
        docker.enabled = true
        process {
          withName: index_bam {
            container = "lbmc/sambamba:0.6.7"
            cpus = 4
          }
          withName: bam_to_bigwig {
            container = "lbmc/deeptools:3.0.2"
            cpus = 4
          }
        }
      }
      singularity {
        singularity.enabled = true
        singularity.cacheDir = "./bin/"
        process {
          withName: index_bam {
            container = "lbmc/sambamba:0.6.7"
            cpus = 4
          }
          withName: bam_to_bigwig {
            container = "lbmc/deeptools:3.0.2"
            cpus = 4
          }
        }
      }
      psmn{
        singularity.enabled = true
        singularity.cacheDir = "/.singularity_psmn/"
        singularity.runOptions = "--bind /Xnfs,/scratch"
        process{
          withName: index_bam {
            container = "lbmc/deeptools:3.0.2"
            executor = "sge"
            clusterOptions = "-cwd -V"
            cpus = 32
            memory = "30GB"
            time = "24h"
            queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
            penv = "openmp32"
          }
        }
      }
      ccin2p3 {
        singularity.enabled = true
        singularity.cacheDir = "$baseDir/.singularity_in2p3/"
        singularity.runOptions = "--bind /pbs,/sps,/scratch"
        process{
          withName: index_bam {
            container = "lbmc/sambamba:0.6.7"
            scratch = true
            stageInMode = "copy"
            stageOutMode = "rsync"
            executor = "sge"
            clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
            "
            cpus = 1
            queue = "huge"
          }
          withName: bam_to_bigwig {
            container = "lbmc/deeptools:3.0.2"
            scratch = true
            stageInMode = "copy"
            stageOutMode = "rsync"
            executor = "sge"
            clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
            "
            cpus = 1
            queue = "huge"
          }
        }
      }
    }