nextflow.config

nextflow.enable.dsl = 2
outputDir = 'results'
params {
    input = null
    genome = null

    // Boilerplate options
    outputDir = 'results'
    tracedir = "${params.outputDir}/pipeline_info"
    publish_dir_mode = 'link'

    // Max resource options
    max_memory = '224 GB'
    max_cpus = 32
    max_time = '72 h'
}

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
        singularity.cacheDir = null // overridden by profiles: biowulf, frce, & slurmint
        envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID,SINGULARITY_BINDPATH'
    }
    biowulf {
        includeConfig "conf/biowulf.config"
    }
    slurm {
        includeConfig "conf/slurm.config"
    }
    interactive {
        includeConfig "conf/interactive.config"
    }
    test {
        includeConfig "conf/test.config"
    }
    ci_stub {
        includeConfig "conf/ci_stub.config"
    }
}

includeConfig 'conf/containers.config'
includeConfig 'conf/modules.config'

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
    JULIA_DEPOT_PATH = "/usr/local/share/julia"
}

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

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

plugins {
  id 'nf-schema@2.7.1'
  id 'nf-prov@1.4.0'
}
validation {
    help {
        enabled = true
    }
}
prov {
    enabled = true
    formats {
        bco {
            file = "${params.tracedir}/bco.json"
            overwrite = true
        }
        dag {
            file = "${params.tracedir}/dag.html"
            overwrite = true
        }
    }
}

manifest {
    name = "CCBR/TOOL_NAME"
    author = "CCR Collaborative Bioinformatics Resource"
    homePage = "https://github.com/CCBR/TOOL_NAME"
    description = "TODO one-line description of TOOL_NAME goes here"
    mainScript = "main.nf"
    defaultBranch = "main"
    version = "0.1.0-dev"
}

workflow.output.mode = params.publish_dir_mode