nextflow.config

// Load processes parameters
includeConfig 'conf/base.config'
// Load resources configuration
includeConfig 'conf/resources.config'


// Export Time Zone required for QIIME2 2019.10
env {
  TZ = 'Europe/Paris'
}

manifest {
    name = 'samba'
    author = 'IFREMER-IRSI-SeBiMER'
    description = 'Standardized and Automated MetaBarcoding Analyses workflow developped by Ifremer SeBiMER team'
    homePage = 'https://github.com/ifremer-bioinformatics/samba'
    mainScript = 'main.nf'
    nextflowVersion = '>=20.04.1'
    version = 'v3.1.0'
}

// Execution profiles
profiles {
    shortreadstest { 
        includeConfig 'conf/shortreadstest.config'
        includeConfig 'conf/reports.config'
        // Workdir for temporary data
        workDir = "${baseDir}/work/$params.projectName"
    }
    longreadstest {
        includeConfig 'conf/longreadstest.config'
        includeConfig 'conf/reports.config'
        // Workdir for temporary data
        workDir = "${baseDir}/work/$params.projectName"
    }
    custom {
        includeConfig 'conf/custom.config'
        includeConfig 'conf/reports.config'
        // Workdir for temporary data
        workDir = "${baseDir}/work/$params.projectName"
    }
    conda { 
        docker.enabled = false
        singularity.enabled = false
        createTimeout = '60min'
        process {
            withLabel : qiime2_env1cpu {
                conda = "${baseDir}/containers/qiime2-2019.10/environment.yml"
            }
            withLabel : qiime2_env {
                conda = "${baseDir}/containers/qiime2-2019.10/environment.yml"
            }
            withLabel : qiime2_highRAM {
                conda = "${baseDir}/containers/qiime2-2019.10/environment.yml"
            }
            withLabel : microdecon_env {
                conda = "${baseDir}/containers/microdecon-1.0.2/environment.yml"
            }
            withLabel : r_stats_env {
                conda = "${baseDir}/containers/r-3.6.1/environment.yml"
            }
            withLabel : seqtk_env {
                conda = "${baseDir}/containers/seqtk-1.2/environment.yml"
            }
            withLabel : jinja2_env {
                conda = "${baseDir}/containers/jinja2-2.11.1/environment.yml"
            }
            withLabel : biopython_env {
                conda = "${baseDir}/containers/biopython-1.79/environment.yml"
            }
            withLabel : lr_mapping_env {
                container = "${baseDir}/containers/longreads-1.0/environment.yml"
            }
        }
    }
    docker {
        docker {
             enabled = true
             fixOwnership = true
             runOptions = "-u \$(id -u):\$(id -g)"
        }
        process {
            withLabel : qiime2_env1cpu {
                container = "sebimer/samba-qiime2:2019.10"
            }
            withLabel : qiime2_env {
                container = "sebimer/samba-qiime2:2019.10"
            }
            withLabel : qiime2_highRAM {
                container = "sebimer/samba-qiime2:2019.10"
            }
            withLabel : microdecon_env {
                container = "sebimer/samba-microdecon:1.0.2"
            }
            withLabel : r_stats_env {
                container = "sebimer/samba-r:3.6.1"
            }
            withLabel : seqtk_env {
                container = "sebimer/samba-seqtk:1.2"
            }
            withLabel : jinja2_env {
                container = "sebimer/samba-jinja2:2.11.1"
            }
            withLabel : biopython_env {
                container = "sebimer/samba-v4-biopython:1.79"
            }
            withLabel : lr_mapping_env {
                container = "sebimer/samba-longreads:1.0"
            }
        }

        singularity.enabled = false
    }
    singularity {
        docker.enabled = false
        singularity.autoMounts = true
        singularity.enabled = true
        process {
            withLabel : qiime2_env1cpu {
                container = "sebimer/samba-qiime2:2019.10"
            }
            withLabel : qiime2_env {
                container = "sebimer/samba-qiime2:2019.10"
            }
            withLabel : qiime2_highRAM {
                container = "sebimer/samba-qiime2:2019.10"
            }
            withLabel : microdecon_env {
                container = "sebimer/samba-microdecon:1.0.2"
            }
            withLabel : r_stats_env {
                container = "sebimer/samba-r:3.6.1"
            }
            withLabel : seqtk_env {
                container = "sebimer/samba-seqtk:1.2"
            }
            withLabel : jinja2_env {
                container = "sebimer/samba-jinja2:2.11.1"
            }
            withLabel : biopython_env {
                container = "sebimer/samba-v4-biopython:1.79"
            }
            withLabel : lr_mapping_env {
                container = "sebimer/samba-longreads:1.0"
            }
        }
    }
}

// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
  if (type == 'memory') {
    try {
      if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
        return params.max_memory as nextflow.util.MemoryUnit
      else
        return obj
    } catch (all) {
      println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
      return obj
    }
  } else if (type == 'time') {
    try {
      if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
        return params.max_time as nextflow.util.Duration
      else
        return obj
    } catch (all) {
      println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
      return obj
    }
  } else if (type == 'cpus') {
    try {
      return Math.min( obj, params.max_cpus as int )
    } catch (all) {
      println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
      return obj
    }
  }
}