nextflow.config

profiles {

	standard {
      process {
        executor = 'local'
        // Process specific configuration
        withName: cutadapt {
          module = ['system/Python-3.6.3']
          cpus = 8
          memory = { 8.GB * task.attempt }
        }
        withName: sickle {
          module = ['bioinfo/sickle-1.33']
          memory = { 8.GB * task.attempt }
        }
        withLabel: fastqc {
          module = ['bioinfo/FastQC_v0.11.7']
          cpus = 8
          memory = { 8.GB * task.attempt }
        }
        withName: multiqc {
          module = ['bioinfo/multiqc-v1.5']
          memory = { 8.GB * task.attempt }
        }
        withName: alignment_filter {
        module = ['/work/jfourquet/antiselfish/data_test/bioinfo_bwa_samtools']
        memory = { 100.GB * task.attempt }
        cpus = 8
        }
        withName: index_db_kaiju {
        memory = { 40.GB * task.attempt }
				module = ['bioinfo/kaiju-v1.7.0']
        cpus = 5
        time = '24h'
        }
        withName: kaiju {
        module = ['bioinfo/KronaTools-2.7','system/R-3.5.2','bioinfo/kaiju-v1.7.0']
        memory = { 100.GB * task.attempt }
        cpus = 25
        }
        withName: metaspades {
        module = ['bioinfo/SPAdes-3.11.1']
        memory = { 100.GB * task.attempt }
        }
        withName: megahit {
        module = ['bioinfo/megahit_v1.1.3']
        cpus = 48
        memory = { 100.GB * task.attempt }
        }
        withName: prokka {
        module = ['bioinfo/prokka-1.13.4']
        memory = { 100.GB * task.attempt }
        }
        withLabel: cd_hit {
        module = ['bioinfo/cdhit-4.6.8']
        memory = { 100.GB * task.attempt }
        }
        withLabel: cd_hit_produce_table {
        memory = { 4.GB * task.attempt }
        }
        withName: quantification {
        module = ['/work/jfourquet/antiselfish/data_test/bioinfo_bwa_samtools_subread']
        memory = { 100.GB * task.attempt }
        }
				withLabel: python {
				module = ['system/Python-3.6.3']
        memory = { 4.GB * task.attempt }
        }
      }
    }
    cluster_slurm {
      process {
        executor = 'slurm'
        // Process specific configuration
				withName: cutadapt {
					module = ['system/Python-3.6.3']
					cpus = 8
					memory = { 8.GB * task.attempt }
				}
				withName: sickle {
					module = ['bioinfo/sickle-1.33']
					memory = { 8.GB * task.attempt }
				}
				withLabel: fastqc {
					module = ['bioinfo/FastQC_v0.11.7']
					cpus = 8
					memory = { 8.GB * task.attempt }
				}
				withName: multiqc {
					module = ['bioinfo/multiqc-v1.5']
					memory = { 8.GB * task.attempt }
				}
				withName: alignment_filter {
				module = ['/work/jfourquet/antiselfish/data_test/bioinfo_bwa_samtools']
				memory = { 100.GB * task.attempt }
				queue = 'unlimitq'
				cpus = 8
				}
				withName: index_db_kaiju {
				memory = { 200.GB * task.attempt }
				module = ['bioinfo/kaiju-v1.7.0']
				cpus = 5
				time = '24h'
				}
				withName: kaiju {
				module = ['bioinfo/KronaTools-2.7','system/R-3.5.2','bioinfo/kaiju-v1.7.0']
				memory = { 100.GB * task.attempt }
				cpus = 25
				}
				withName: metaspades {
				module = ['bioinfo/SPAdes-3.11.1']
				memory = { 100.GB * task.attempt }
				queue = 'unlimitq'
				cpus = 48
				}
				withName: megahit {
				module = ['bioinfo/megahit_v1.1.3']
				cpus = 48
				memory = { 100.GB * task.attempt }
				queue = 'unlimitq'
				}
				withName: prokka {
				module = ['bioinfo/prokka-1.13.4']
				memory = { 100.GB * task.attempt }
				queue = 'unlimitq'
				cpus = 16
				}
				withLabel: cd_hit {
				module = ['bioinfo/cdhit-4.6.8']
				memory = { 100.GB * task.attempt }
				}
				withLabel: cd_hit_produce_table {
				memory = { 4.GB * task.attempt }
				}
				withName: quantification {
				module = ['/work/jfourquet/antiselfish/data_test/bioinfo_bwa_samtools_subread']
				memory = { 100.GB * task.attempt }
				}
				withLabel: python {
				module = ['system/Python-3.6.3']
				memory = { 4.GB * task.attempt }
				}
      }
    }
}