nextflow.config

//
// Notes to End Users.
//
// The workflow should run without editing this configuration file,
// however there may be instances in which you wish to edit this
// file for compute performance or other reasons. Please see:
//
//   https://nextflow.io/docs/latest/config.html#configuration
//
// for further help editing this file.

params {
    help                 = false
    version              = false
    out_dir              = "output"
    artic_threads        = 4
    squirrel_threads     = 4
    squirrel_options     = false
    analyse_unclassified = false
    skip_squirrel        = false

    fastq                = null
    sample               = null
    sample_sheet         = null
    min_reads            = 1000
    min_len              = null
    max_len              = null
    max_softclip_length  = null
    normalise            = 200
    override_model       = null
    scheme_name          = "MPXV"
    scheme_version       = "yale-mpox/v1.0.0-cladeI"
    list_schemes         = false
    custom_scheme        = null
    aws_image_prefix     = null
    aws_queue            = null
    disable_ping         = false
    lab_id               = null
    testkit              = null

    monochrome_logs      = false
    validate_params      = true
    show_hidden_params   = false
    schema_ignore_params = 'show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf'

    wf {
        example_cmd   = [
            "--fastq 'wf-artic-demo/fastq'",
            "--sample_sheet 'wf-artic-demo/sample_sheet.csv'",
            "--scheme_name 'SARS-CoV-2'",
            "--scheme_version 'Midnight-ONT/V3'"
        ]
        common_sha    = 'sha8b5843d549bb210558cbb676fe537a153ce771d6'
        container_sha = 'sha15e9dfa0469ddd0641dfe1a5f07bedb475a8a03d'
    }
}

manifest {
    name            = 'artic-network/artic-mpxv-nf'
    author          = 'Oxford Nanopore Technologies. artic-network: Sam Wilkinson, Rachel Colquhoun'
    homePage        = 'https://github.com/artic-network/artic-mpxv-nf'
    description     = 'Run the ARTIC fieldbioinformatics workflow on multiplexed MPXV ONT data'
    mainScript      = 'main.nf'
    nextflowVersion = '>=23.04.2'
    version         = 'v1.2.8'
}

epi2melabs {
    tags = 'mpox,artic,amplicon,viruses,public health'
    icon = 'faVirusCovid'
}


env {
    PYTHONNOUSERSITE  = 1
    JAVA_TOOL_OPTIONS = "-Xlog:disable -Xlog:all=warning:stderr"
}

process {
    withLabel: wf_common {
        container = "ontresearch/wf-common:${params.wf.common_sha}"
        memory    = '1G'
        conda     = "nanoporetech::fastcat bioconda::tabix"
    }
    withLabel: artic {
        container = "quay.io/artic/fieldbioinformatics:1.5.3"
        memory    = { 4.GB * task.attempt }
        conda     = "bioconda::artic=1.5.3"
    }
    withLabel: squirrel {
        container = "articnetworkorg/squirrel@sha256:6311a61f667fa288b7ede67e88f4b7451e31f8b1da3ac61c5d1c8f303e253591"
        memory    = '2G'
        conda     = "bioconda::squirrel=1.0.12"
    }
    shell = ['/bin/bash', '-euo', 'pipefail']
}

profiles {

    // the "standard" profile is used implicitely by nextflow
    // if no other profile is given on the CLI
    standard {
        docker {
            enabled    = true
            // this ensures container is run as host user and group, but
            //    also adds host user to the within-container group
            runOptions = '--user $(id -u):$(id -g) --group-add 100 --platform linux/amd64'
        }
    }

    conda {
        conda.enabled        = true
        docker.enabled       = false
        singularity.enabled  = false
        podman.enabled       = false
        shifter.enabled      = false
        charliecloud.enabled = false
        apptainer.enabled    = false
    }

    mamba {
        conda.enabled        = true
        conda.useMamba       = true
        docker.enabled       = false
        singularity.enabled  = false
        podman.enabled       = false
        shifter.enabled      = false
        charliecloud.enabled = false
        apptainer.enabled    = false
    }

    awsbatch {
        process {
            executor = 'awsbatch'
            queue    = "${params.aws_queue}"
            withLabel: wf_common {
                container = "${params.aws_image_prefix}-wf-common:${params.wf.common_sha}"
                memory    = '1G'
            }
            withLabel: artic {
                container = "${params.aws_image_prefix}-wf-artic:${params.wf.container_sha}"
                memory    = '2G'
            }
            shell    = ['/bin/bash', '-euo', 'pipefail']
        }
    }

    local {
        process.executor = 'local'
    }
}

timeline {
    enabled   = true
    overwrite = true
    file      = "${params.out_dir}/execution/timeline.html"
}
report {
    enabled   = true
    overwrite = true
    file      = "${params.out_dir}/execution/report.html"
}
trace {
    enabled   = true
    overwrite = true
    file      = "${params.out_dir}/execution/trace.txt"
}