nextflow.config

#!/usr/bin/env nextflow
nextflow.enable.dsl=2

// Configuration File
manifest {
    author = 'Phelelani Mpangase'
    homePage = 'https://github.com/phelelani/nf-rnaSeqCount'
    description = 'rnaSeqCount pipeline'
    mainScript = 'main.nf'
    version = '0.2'
}

// CHECK INPUTS AND OUTPUTS:
params {
    help       = null
    workflow   = null
    runOptions = ""
}

// SINGULARITY OPTIONS
singularity {
    enabled = true
    autoMounts = true
    cacheDir = "$HOME/.singularity/cache"
    runOptions = "${params.runOptions}" + " --cleanenv"
}

// ALL PROCESSESS SETTINGS
process {
    // ALL PROCESSES
    cache        = true
    scratch      = false
    stageInMode  = 'symlink'
    stageOutMode = 'rsync'

    // DEFAULT RESOURCES
    cpus         = 1
    memory       = 4.GB
    time         = 24.h
    
    // CONTAINERS AND RESOURCES
    withLabel: 'star' {
        cpus = 32
        memory = 128.GB
        time = 48.h
        container = 'docker://phelelani/nf-rnaseqcount:star'
    }
    withLabel: 'bowtie' {
        cpus = 32
        memory = 128.GB
        time = 48.h        
        container = 'docker://phelelani/nf-rnaseqcount:bowtie2'
    }
    withLabel: 'fastqc' {
        container = 'docker://phelelani/nf-rnaseqcount:fastqc'
    }
    withLabel: 'trimmomatic' {
        cpus = 32
        memory = 128.GB
        time = 48.h        
        container = 'docker://phelelani/nf-rnaseqcount:trimmomatic'
    }
    withLabel: 'htseqcount' {
        container = 'docker://phelelani/nf-rnaseqcount:htseqcount'
    }
    withLabel: 'featurecounts' {
        cpus = 16
        memory = 32.GB
        time = 48.h
        container = 'docker://phelelani/nf-rnaseqcount:featurecounts'
    }
    withLabel: 'multiqc' {
        container = 'docker://phelelani/nf-rnaseqmetagen:multiqc'
    }
}

// PIPELINE TRACING, VISUALIZATION AND HELP
def pipelineHelp() {
    if (params.help || params.workflow == null) {
    } else if (params.workflow in [ 'genome-indexing', 'read-qc', 'read-trimming', 'read-alignment', 'read-counting' ]) {
        trace {
            enabled = true
            overwrite = true
            file = "${launchDir}/exec_report/${params.workflow}_trace.txt"
        }
        timeline {
            enabled = true
            overwrite = true
            file = "${launchDir}/exec_report/${params.workflow}_timeline.html"
        }
        report {
            enabled = true
            overwrite = true
            file = "${launchDir}/exec_report/${params.workflow}_report.html"
        }
    } else {}
}

// PROFILES AND PROCESS OPTIONS
profiles {
    standard {
        process.executor = 'local'
        pipelineHelp()
    }
    wits {
        process.executor = 'slurm'
        process.queue = 'batch'
        pipelineHelp()
    }
    ilifu {
        process.executor = 'slurm'
        process.queue = 'Main'
        pipelineHelp()
    }
}