nextflow.config

// Global default params, used in configs
params {
    // Workflow flags
    reads = null
    outdir = "results"
    sample_size = 10000

    // Boilerplate options
    publish_dir_mode = 'copy'
    enable_conda = false
    singularity_pull_docker_container = false
}

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

profiles {
    debug { process.beforeScript = 'echo $HOSTNAME' }
    docker {
        docker.enabled = true
        // Avoid this error:
        //   WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
        // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
        // once this is established and works well, nextflow might implement this behavior as new default.
        docker.runOptions = '-u \$(id -u):\$(id -g)'
    }
    singularity {
        singularity.enabled = true
        singularity.autoMounts = true
    }
    test {
        params.reads = "test_data/*.fastq.gz"
        params.sample_size = 100
        params.max_memory = 4.GB
    }
}

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER = "/.Rprofile"
    R_ENVIRON_USER = "/.Renviron"
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
    enabled = true
    file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.svg"
}

manifest {
    name = 'subsample-fastq'
    author = 'Lorena Pantano'
    homePage = 'https://github.com/your-github-account/your-pipeline-repo'
    description = 'Nextflow pipeline for subsampling FASTQ files using seqtk'
    mainScript = 'main.nf'
    nextflowVersion = '>=20.04.0'
    version = '1.0.0'
}

// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
    if (type == 'memory') {
        try {
            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                return params.max_memory as nextflow.util.MemoryUnit
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'time') {
        try {
            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                return params.max_time as nextflow.util.Duration
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (all) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}