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building_your_pipeline.md

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  • bam_to_bigwig.config 1.07 KiB
    profiles {
      docker {
        docker.temp = 'auto'
        docker.enabled = true
        process {
          withName: index_bam {
            container = "sambamba:0.6.7"
          }
          withName: bam_to_bigwig {
            container = "deeptools:3.0.2"
          }
        }
      }
      psmn {
        process{
          withName: index_bam {
            beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
            module = "sambamba/0.6.7"
            executor = "sge"
            clusterOptions = "-m e -cwd -V"
            memory = "30GB"
            time = "24h"
            queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
            penv = 'openmp16'
          }
          withName: bam_to_bigwig {
            beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
            module = "deepTools/3.0.2"
            executor = "sge"
            clusterOptions = "-m e -cwd -V"
            memory = "30GB"
            time = "24h"
            queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
            penv = 'openmp16'
          }
        }
      }
    }