nextflow.config

// EXECUTION DEFAULTS A PROJECT MAY REPLACE, and they are above the include below for that
// reason: Nextflow is later-wins, so the same assignment placed after parameters.config was
// read would beat whatever the project asked for, silently. Anything here reads no parameter,
// which is what lets it sit this high.
conda.enabled = true
docker.enabled = false

// Remove the work/ directory once the run completes successfully.
// `cleanup` is a plain option, not a config scope - do not add a `cleanup { }` block.
cleanup = true

process {
    errorStrategy = 'finish'  // Options: 'ignore', 'terminate', 'retry'
    maxRetries = 3
    maxErrors = -1  // -1 means unlimited; set to number to stop after N errors
}

// Your project's settings, read from the directory you launch the run in. `${launchDir}`, not a
// bare name, which would resolve against this file and find only a config inside the
// installation.
//
// This include must stay ABOVE everything that reads a parameter: config interpolation is a
// single forward pass.
includeConfig "${launchDir}/parameters.config"

// Guarantees the `cores` scope exists as a map. parameters.config carries the block with every
// key commented out, and a scope containing only comments creates nothing; a module cannot make
// a top-level params key that processes can see, so it is made here, at config time.
//
// A ternary and not an `if`: the strict parser rejects `if` statements in config.
params.cores = params.containsKey('cores') && params.cores != null ? params.cores : [:]

// A dry run checks and previews instead of computing. Set by `./PoolSeqFlow dryrun`, which also
// runs dryrun.nf: the entry script stops the pipeline, this flag stops step 0 recording anything.
params.dryRun = false

// Where the preview goes: the project directory, beside parameters.config, out of both storage
// roots. `./PoolSeqFlow dryclean` asks this same value where to look.
params.dryRunDir = "${launchDir}/dryrun"

// Pipeline identity. `version` is what Nextflow reports and what step 0 records in each project.
// One of three places the version lives, with `VERSION=` and the `# Version:` header in
// ./PoolSeqFlow; dev/scripts/bump-version.sh updates all three.
manifest {
    name            = 'PoolSeqFlow'
    author          = 'Ozan L. Z. Kiratli'
    description     = 'Allele frequency analysis from pooled Illumina sequencing data'
    homePage        = 'https://ozankiratli.github.io/PoolSeqFlow/'
    mainScript      = 'poolseqflow.nf'
    license         = 'Apache-2.0'
    doi             = '10.5281/zenodo.19245611'
    version         = '3.2.0'
    // Advisory: Nextflow warns and carries on. Prefixing with `!` would make it abort.
    nextflowVersion = '>=26.04.0'
}

// Below the include, because it reads two parameters. A project cannot replace this block and
// does not need to: both numbers in it are its own.
process {
    // Ceiling for what a task may request. Clamps; does not allocate.
    resourceLimits = [
        memory: params.memory,
        cpus: params.threads
    ]
}

dag {
    enabled = true
    file = "${params.dir.sessionReports}/PoolSeqFlow_pipeline_dag.html"
    overwrite = true
}

trace {
    enabled = true
    file = "${params.dir.sessionReports}/PoolSeqFlow_pipeline_trace.txt"
    sep = '\t'
    raw = true
    fields = [
        'status',
        'task_id',
        'hash',
        'name',
        'exit',
        'start',
        'complete',
        'duration',
        'realtime',
        'cpus',
        'memory',
        '%cpu',
        '%mem',
        'attempt'
    ]
    overwrite = true
}

timeline {
    enabled = true
    file = "${params.dir.sessionReports}/PoolSeqFlow_pipeline_timeline.html"
    overwrite = true
}

report {
    enabled = true
    file = "${params.dir.sessionReports}/PoolSeqFlow_pipeline_report.html"
    overwrite = true
}

// Under mainDir; a relative path would resolve against the launch directory.
workDir = "${params.mainDir}/work"


env {
    PATH="${params.dir.bin}:\$PATH"
}