nextflow.config

manifest {
    name = 'SNP&SEQ Run folder QC pipeline'
    author = 'SNP&SEQ Bioinformatics Team; Mahesh Binzer-Panchal'
    homePage = ''
    description = 'A Nextflow run folder QC pipeline for SciLifeLab SNP&SEQ platform'
    mainScript = 'main.nf'
    nextflowVersion = '!>=21.04.1'
    version = '1.2.0'
}

profiles {

    debug { process.beforeScript = 'env'}

    dev {
        executor.name = 'local'
        executor.memory = '12G'
        includeConfig "$baseDir/config/nextflow_config/compute_resources.config"

        // Overwrite high_memory label
        process {
            withLabel: 'high_memory' {
                memory = '12G'
            }
        }
    }

    uppmax {
        process {
            shell = ['/bin/bash', '-euo', 'pipefail']
            errorStrategy = { task.exitStatus in [255] ? 'retry' : 'terminate' }
            maxRetries = 2
            scratch = true
            executor = 'slurm'
            clusterOptions = { "-A $params.project" }
            cpus = 1
            memory = '8G'
            time = '3h'
        }
        includeConfig "$baseDir/config/nextflow_config/compute_resources.config"
    }

    snpseq {
        executor {
            name = 'local'
            cpus = 8
            memory = '47G'
        }
        process {
            shell = ['/bin/bash', '-euo', 'pipefail']
            errorStrategy = { task.exitStatus in [255] ? 'retry' : 'terminate' }
            maxRetries = 2
            cpus = 1
        }
        includeConfig "$baseDir/config/nextflow_config/compute_resources.config"
    }

    singularity { 
        includeConfig 'config/nextflow_config/singularity.config'
    }

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