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fastqdump.nf

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  • Forked from LBMC / nextflow
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    indexing.config 1.66 KiB
    profiles {
      docker {
        docker.temp = 'auto'
        docker.enabled = true
        process {
          withName: index_fasta {
            container = "bowtie2:2.3.4.1"
            cpus = 4
          }
        }
      }
      singularity {
        singularity.enabled = true
        process {
          withName: index_fasta {
            container = "file://bin/bowtie2:2.3.4.1.img"
            cpus = 4
          }
        }
      }
      psmn{
        process{
          withName: index_fasta {
            beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
            module = "bowtie2/2.3.4.1"
            executor = "sge"
            clusterOptions = "-cwd -V"
            cpus = 16
            memory = "20GB"
            time = "12h"
            queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
            penv = 'openmp16'
          }
        }
      }
      ccin2p3_conda {
        process{
          withName: index_fasta {
            beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
            conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
            scratch = true
            stageInMode = "copy"
            stageOutMode = "rsync"
            executor = "sge"
            clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
            "
            cpus = 1
            queue = 'huge'
          }
        }
      }
      ccin2p3 {
        singularity.enabled = true
        singularity.runOptions = "--bind /pbs,/sps,/scratch"
        process{
          withName: index_fasta {
            container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
            scratch = true
            stageInMode = "copy"
            stageOutMode = "rsync"
            executor = "sge"
            clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
            cpus = 1
            queue = 'huge'
          }
        }
      }
    }