nextflow.config

/*
 * -------------------------------------------------
 *  Pipeline config
 * -------------------------------------------------
 */

// Global default params
params {
    // Trimming
    skip_trimming              = false
    save_trimmed               = false

    // Transcript quantification
    fragment_len               = 150 
    fragment_sd                = 20
    strandedness               = 2

    // Gene subsetting
    perc                       = 99

    // Normalisation
    norm_method                = 'DESeq'

    // Grouping strains
    group                      = 'majority_ST'

    // Options: Other
    help                       = false
    name                       = false   // optional name for the pipeline run
    outdir                     = './results'
    cachedir                   = './'

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory                 = '192.GB'
    max_cpus                   = 56
    max_time                   = '10000.h'

    // Config options
    config_profile_name        = null

}


profiles {
    conda {
        params.enable_conda    = true
        process.conda          = "$baseDir/environment.yml"
        conda.createTimeout    = '2 h'
        // includeConfig 'configs/container.config'
    }
    slurm {
        workDir                = params.workdir
        executor.name          = "slurm"
        executor.queueSize     = 200
        params.cloudProcess    = true
        process.cache          = "lenient"
        // includeConfig 'configs/container.config'
    }
    docker {
        process.container      = 'adamd3/strainseq:latest'
        docker {
            enabled            = true
            userEmulation      = true
            runOptions         = '--pull=always'
        }
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        // includeConfig 'configs/container.config'
    }
    singularity {
        process.container      = 'adamd3/strainseq:latest'
        singularity {
            enabled            = true
            cacheDir           = params.cachedir
            autoMounts         = true
            runOptions         = "--bind $PWD"
        }
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        // singularity_pull_docker_container = false
        // includeConfig 'configs/container.config'
    }
    cambridge {
        process.container      = 'adamd3/strainseq:latest'
        singularity {
            enabled            = true
            cacheDir           = params.cachedir
            autoMounts         = true
            runOptions         = "--bind $PWD"
        }
        process {
            executor           = 'slurm'
            clusterOptions     = '-p cclake'
            cache              = "lenient"
        }
        params {
            max_memory         = 192.GB
            max_cpus           = 56
        }
        // includeConfig 'configs/container.config'
    }
    test      { 
        process.container      = 'adamd3/strainseq:latest'
        docker {
            enabled            = true
            userEmulation      = true
            runOptions         = '--pull=always'
        }
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        includeConfig 'configs/test.config'     
        }
}

// Export these variables to prevent local Python/R libraries from 
// conflicting with those in the container
env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
}

// Default configuration for the processes in the pipeline
process {
    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
    memory = { check_max( 6.GB * task.attempt, 'memory' ) }

    errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
    maxRetries    = 1
    maxErrors     = '-1'

    // Capture exit codes from upstream processes when piping
    shell = ['/bin/bash', '-euo', 'pipefail']

    // Process-specific resource requirements
    withLabel:process_low {
        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
    }
    withLabel:process_medium {
        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
    }
    withLabel:process_high {
        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
    }
}


// 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: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (all) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}