nextflow.config

// default params
params {
    outdir = 'out'
    input = ''

    //cogaps params
    npatterns = 8
    nsets = 7
    niterations = 100
    sparse = 1
    seed = 42
    distributed = 'null'
    nthreads = 1

    max_memory = '8.GB'
    max_cpus = 4
    max_time = '48.h'
}

//reporting
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
    enabled = true
    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}

//output
process {
    publishDir = { "${params.outdir}" }
}

//resources
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
        }
    }
}

process {
    /*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    btc/spatial Nextflow base config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    A 'blank slate' config file, appropriate for general use on most high performance
    compute environments. Assumes that all software is installed and available on
    the PATH. Runs in `local` mode - all jobs will be run on the logged in environment.
----------------------------------------------------------------------------------------
    */

    // TODO nf-core: Check the defaults for all processes
    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
    time   = { check_max( 4.h  * task.attempt, 'time'   ) }

    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
    maxRetries    = 1
    maxErrors     = '-1'

    // Process-specific resource requirements
    // NOTE - Please try and re-use the labels below as much as possible.
    //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
    //        If possible, it would be nice to keep the same label naming convention when
    //        adding in your local modules too.
    // TODO nf-core: Customise requirements for specific processes.
    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
    withLabel:process_single {
        cpus   = { check_max( 1                  , 'cpus'    ) }
        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
    }
    withLabel:process_low {
        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
    }
    withLabel:process_medium {
        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
    }
    withLabel:process_high {
        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
    }
    withLabel:process_long {
        time   = { check_max( 48.h  * task.attempt, 'time'    ) }
    }
    withLabel:process_high_memory {
        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
    }
    withLabel:error_ignore {
        errorStrategy = 'ignore'
    }
    withLabel:error_retry {
        errorStrategy = 'retry'
        maxRetries    = 2
    }
}

// profiles to run the pipeline
profiles {
    docker {
        docker.enabled         = true
    }

    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
    }

    slurm {
        singularity.enabled =    true
        singularity.autoMounts = true
        process {
            executor = 'slurm'
            cpus = 10
            memory = '10 GB'
        }
    }
    test {
        process {
            withName: COGAPS {
                cpus = 1
            }
        }
    }
}