nextflow.config

params {
    input = "${projectDir}/assets/samplesheet.csv"
    fasta = "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz"
    gene_bed = "s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed"
    gtf = "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/hg19.refGene.gtf.gz"
    chrom_len = "https://genome.ucsc.edu/goldenPath/help/hg19.chrom.sizes"
    adapter_sequence = "TCGTATCCCGTCTTCTGCTTG"
}

plugins {
  id 'nf-schema@2.1.0'
}

profiles {
    test {
        params.input = "https://raw.githubusercontent.com/nf-core/nascent/master/assets/samplesheet.csv"
        params.fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21.fa'
        params.gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/genes_chr21.gtf'

        docker.enabled = true
        wave.enabled = true
        process.conda = "${projectDir}/environment.yml"
        // FIXME need to login
        wave.freeze = false
    }
    utd_ganymede {
        includeConfig "https://raw.githubusercontent.com/nf-core/configs/master/conf/utd_ganymede.config"
        wave.enabled = true
        // wave.freeze = true
        // wave.build.repository = 'ghcr.io/functional-genomics-lab/active-enhancers'
        process.conda = "${projectDir}/environment.yml"
        singularity.registry = 'quay.io'
        process {
            cpus = 16
            memory = 26.GB
            time = 24.h
            withName: "GROHMM_TRANSCRIPTCALLING" {
                cpus = 12
                memory = 100.GB
            }
        }
    }
}