nextflow-code/nextflow.config at main · SimranChhabria/nextflow-code · GitHub

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// Load processes parameters

includeConfig 'configs/base.config'
//includeConfig 'configs/input.config'
//includeConfig 'configs/onco-ref.config'

params {
    // Workflow flags:

    // Mandatory arguments
    def run_name            = params.run_name
    def runid               = params.runid
    def ref_dir             = "${launchDir}/data/wuhan_ref"

    metadir                 = "${launchDir}/data/meta_info"
    samplesheetBCL          = "${metadir}/${run_name}_sample_sheet.csv"
    samplesheetmeta         = "${metadir}/${run_name}_meta_sheet.csv"


    inputfastq              = "${launchDir}/data/${params.run_name}/*_R{1,2}_001.fastq.gz"
    outdir                  = "${launchDir}/data/${params.run_name}/results"
    wuhan_ref               = "${ref_dir}/wuhan_trim3polyA.fasta"
    genome_gff              = "${ref_dir}/GCF_009858895.2_ASM985889v3_genomic.gff"


    // Main options
    publish_dir_mode       = 'copy'
    no_intervals           = false      // Intervals will be built from the fasta file
    nucleotides_per_second = 1000       // Default interval size
    tools                  = null       // No default Variant_Calling or Annotation tools
    skip_tools             = null       // All tools (markduplicates + baserecalibrator + QC) are used by default
    split_fastq            = 50000000   // FASTQ files will not be split by default by FASTP

    // Modify fastqs (trim/split) with FASTP
    trim_fastq          = true // No trimming
    clip_r1             = 0
    clip_r2             = 0
    three_prime_clip_r1 = 0
    three_prime_clip_r2 = 0
    trim_nextseq        = 0
    save_trimmed        = false
    save_split_fastqs   = false

    //Modify the alignment with BOWTIE2
    save_unaligned     = false
    skip_variants      = false
    min_mapped_reads   = 1000
    }

profiles {
    conda {
        params.enable_conda    = true
        charliecloud.enabled   = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        singularity.enabled    = false
    }
    docker {
        docker.enabled         = true
        //docker.userEmulation   = { params.use_gatk_spark ? false : true }.call()
        charliecloud.enabled   = false
        podman.enabled         = false
        shifter.enabled        = false
        singularity.enabled    = false
    }
    singularity {
        singularity.autoMounts = true
        singularity.enabled    = true
        charliecloud.enabled   = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
    }
}

// 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
        }
    }
}