rnaseq-nextflow-pipeline/nextflow.config at main · Ekin-Kahraman/rnaseq-nextflow-pipeline · GitHub

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/*
 * RNA-seq Pipeline Configuration
 */

params {
    samplesheet   = "${projectDir}/assets/samplesheet.csv"
    genome_index  = null
    gtf           = null
    outdir        = "results"
    strandedness  = 2            // featureCounts: 0=unstranded, 1=forward, 2=reverse
    ref_condition = "untreated"  // DESeq2 reference level for contrast
    aws_queue     = null
    aws_region    = "eu-west-2"
    aws_workdir   = null
}

process {
    cpus = 4
    memory = '8 GB'
    errorStrategy = { task.exitStatus in [137, 143] ? 'retry' : 'finish' }
    maxRetries = 2
}

timeline {
    enabled = true
    file = "${params.outdir}/pipeline_info/timeline.html"
}

report {
    enabled = true
    file = "${params.outdir}/pipeline_info/report.html"
}

trace {
    enabled = true
    file = "${params.outdir}/pipeline_info/trace.txt"
}

dag {
    enabled = true
    file = "${params.outdir}/pipeline_info/dag.dot"
}

profiles {
    docker {
        docker.enabled = true
        docker.runOptions = '--platform linux/amd64'
    }

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

    test {
        params.samplesheet = "${projectDir}/test/samplesheet.csv"
        params.genome_index = "${projectDir}/test/genome"
        params.gtf = "${projectDir}/test/genes.gtf"
        params.strandedness = 0  // synthetic data is unstranded
        params.ref_condition = "negative"

        process {
            cpus = 1
            memory = '2 GB'
        }
    }

    awsbatch {
        docker.enabled = true
        process.executor = 'awsbatch'
        process.queue = params.aws_queue
        aws.region = params.aws_region
        workDir = params.aws_workdir
    }
}

manifest {
    name = 'rnaseq-nextflow-pipeline'
    author = 'Ekin Kahraman'
    description = 'Bulk RNA-seq pipeline: FastQC, fastp, HISAT2, featureCounts, DESeq2, MultiQC'
    version = '1.0.0'
    nextflowVersion = '>=24.0'
    mainScript = 'main.nf'
}