nextflow.config

params {
    genome  = "${baseDir}/data/genome.fa.gz" 
    input   = "${baseDir}/assets/samplesheet.csv" 
    outdir  = "results"
}

process {
    executor = 'local'
    cpus = 4
}

profiles {
    singularity {
        singularity.enabled     = true
        singularity.autoMounts  = true
        docker.enabled          = false
        apptainer.enabled       = false
        conda.enabled           = false
    }

    docker {
        docker.enabled          = true
        docker.userEmulation    = true
        singularity.enabled     = false
        apptainer.enabled       = false
        conda.enabled           = false
    } 

    apptainer {
        apptainer.enabled       = true
        apptainer.autoMounts    = true
        singularity.enabled     = false
        docker.enabled          = false
        conda.enabled           = false
    }

    conda {
        conda.enabled          = true
        docker.enabled         = false
        singularity.enabled    = false
        apptainer.enabled      = false
    }

    cluster {
        process {
            executor = 'slurm'
            memory = '8 GB' 
            time = '30 min'
            cpus = 16    
 
            withLabel: big {
               cpus = 8
                memory = '16 GB'
            }
        }
    }

    test {  includeConfig 'conf/test.config' }
}

// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry   = 'quay.io'
docker.registry      = 'quay.io'
podman.registry      = 'quay.io'
singularity.registry = 'quay.io'

plugins {
    id 'nf-validation@1.1.3'
    id 'nf-iridanext@0.2.0'
    }

iridanext {
    enabled = true
    output {
        path = "${params.outdir}/iridanext.output.json.gz"
        overwrite = true
        files {
            samples = [
                "**/Aligned.sortedByCoord.out.bam",
                "**/Aligned.sortedByCoord.out.bam.bai,"
            ]
        }
    }
}

manifest {
    name            = 'kylacochrane/nf-explore'
    author          = """Kyla Cochrane"""
    homePage        = 'https://github.com/kylacochrane/nf-explore'
    description     = """STAR RNA-seq mapping pipeline"""
    mainScript      = 'main.nf'
    nextflowVersion = '!>=23.04.0'
    version         = '1.0.0.dev'
    doi             = ''
    defaultBranch   = 'main'
}