opal_inform_stitch/nextflow.config at main · BioimageAnalysisCoreWEHI/opal_inform_stitch · GitHub

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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    BioimageAnalysisCoreWEHI/opal_inform_stitch Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {

    // Input/output options
    base_dir                     = null
    outdir                       = null
    publish_dir_mode             = 'copy'

    // ROI finder options
    roi_finder                   = false
    roi_scale                    = 8

    // Boilerplate options
    monochrome_logs              = false
    help                         = false
    version                      = false

    // Schema validation default options
    validate_params              = true
}

profiles {
    debug {
        dumpHashes              = true
        process.beforeScript    = 'echo $HOSTNAME'
        cleanup                 = false
        nextflow.enable.configProcessNamesValidation = true
    }
    conda {
        conda.enabled           = true
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        apptainer.enabled       = false
    }
    mamba {
        conda.enabled           = true
        conda.useMamba          = true
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        apptainer.enabled       = false
    }
    singularity {
        singularity.enabled     = true
        singularity.autoMounts  = true
        conda.enabled           = false
        docker.enabled          = false
        podman.enabled          = false
        apptainer.enabled       = false
    }
    apptainer {
        apptainer.enabled       = true
        apptainer.autoMounts    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
    }

    // For smaller slides (~150 GB RAM) — targets sml nodes (28 cores, 113GB)
    small {
        process {
            executor = 'slurm'
            queue    = 'regular'

            withLabel: 'process_stitch' {
                cpus   = { 4 }
                memory = { 96.GB * task.attempt }
                time   = { 36.h }
            }
        }
        executor {
            queueSize       = 20
            submitRateLimit = '10 sec'
        }
    }

    // For medium slides (~500 GB RAM) — targets med/il nodes (28-48 cores, 491GB)
    medium {
        process {
            executor = 'slurm'
            queue    = 'regular'

            withLabel: 'process_stitch' {
                cpus   = { 8 }
                memory = { 240.GB * task.attempt }
                time   = { 36.h }
            }
        }
        executor {
            queueSize       = 20
            submitRateLimit = '10 sec'
        }
    }

    // For large slides (~1 TB RAM) — targets lrg nodes (64 cores, 1498GB)
    large {
        process {
            executor = 'slurm'
            queue    = 'regular'

            withLabel: 'process_stitch' {
                cpus   = { 12 }
                memory = { 960.GB * task.attempt }
                time   = { 36.h }
            }
        }
        executor {
            queueSize       = 10
            submitRateLimit = '10 sec'
        }
    }
}

// Export these variables to prevent local Python libraries conflicting with conda env
env {
    PYTHONNOUSERSITE = 1
    TMPDIR           = "/vast/scratch/users/\$USER/temp"
}

// Set bash options
process.shell = [
    "bash",
    "-C",         // No clobber - prevent output redirection from overwriting files.
    "-e",         // Exit if a tool returns a non-zero status/exit code
    "-u",         // Treat unset variables and parameters as an error
    "-o",         // Returns the status of the last command to exit..
    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
]

// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false

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}.html"
}

manifest {
    name            = 'BioimageAnalysisCoreWEHI/opal_inform_stitch'
    author          = """WEHI Bioimaging Analysis Core"""
    homePage        = 'https://github.com/BioimageAnalysisCoreWEHI/opal_inform_stitch'
    description     = """Nextflow pipeline for stitching Opal/inForm images from Vectra Polaris in parallel"""
    mainScript      = 'main.nf'
    nextflowVersion = '!>=24.04.2'
    version         = '0.1.0'
}