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multiqc_single.config

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  • multiqc_single.config 2.23 KiB
    profiles {
      docker {
        docker.temp = 'auto'
        docker.enabled = true
        process {
          withName: fastqc_fastq {
            container = "fastqc:0.11.5"
            cpus = 1
          }
          withName: multiqc {
            container = "multiqc:1.7"
            cpus = 1
          }
        }
      }
      singularity {
        singularity.enabled = true
        process {
          withName: fastqc_fastq {
            container = "file://bin/fastqc:0.11.5.img"
            cpus = 1
          }
          withName: multiqc {
            container = "file://bin/multiqc:1.7.img"
            cpus = 1
          }
        }
      }
      psmn {
        process{
          withName: fastqc_fastq {
            beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
            module = "fastqc/0.11.5"
            executor = "sge"
            clusterOptions = "-cwd -V"
            cpus = 1
            memory = "5GB"
            time = "6h"
            queueSize = 1.70
            pollInterval = '60sec'
            queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
          }
          withName: multiqc {
            beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
            module = "multiqc/1.7"
            executor = "sge"
            clusterOptions = "-cwd -V"
            cpus = 1
            memory = "5GB"
            time = "6h"
            queueSize = 1.70
            pollInterval = '60sec'
            queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
          }
        }
      }
      ccin2p3 {
        process{
          withName: fastqc_fastq {
            beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
            conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
            scratch = true
            stageInMode = "copy"
            stageOutMode = "rsync"
            executor = "sge"
            clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
            -o ~/logs/ -e ~/logs/"
            cpus = 1
            queue = 'huge'
          }
          withName: multiqc {
            beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
            conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
            scratch = true
            stageInMode = "copy"
            stageOutMode = "rsync"
            executor = "sge"
            clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
            -o ~/logs/ -e ~/logs/"
            cpus = 1
            queue = 'huge'
          }
        }
      }
    }