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
    fastq = null
    sample = null
    sample_sheet = null
    // Advanced_options
    max_len = null
    min_len = 0
    min_read_qual = null
    min_abundance = 0.0001
    num_alignments = 50
    K = 500000000
    out_dir = "output"
    rank = "species"
    split_tables = false
    counts = false
    store_dir = "store_dir"
    keep_files = false
    keep_counts = false
    keep_read_assignments = false
    output_unclassified = false
    threads = 3
    databases = ['emu', 'silva', 'rdp', 'unite-all', 'unite-fungi']
    database_set = "emu"
    database_sets = [
        'emu': [
            'database': 'osfstorage/emu-prebuilt/emu.tar.gz'
        ],
        'silva': [
            'database': 'osfstorage/emu-prebuilt/silva_database.tar.gz'
        ],
        'rdp': [
            'database': 'osfstorage/emu-prebuilt/rdp.tar.gz'
        ],
        'unite-all': [
            'database': 'osfstorage/emu-prebuilt/unite-all.tar.gz'
        ],
        'unite-fungi': [
            'database': 'osfstorage/emu-prebuilt/unite-fungi.tar.gz'
        ]
    ]

    sample = null
    sample_sheet = null
    analyse_unclassified = false

    wfversion = "v0.0.1"
    wfversion_common = "v0.0.1"
    aws_image_prefix = null
    aws_queue = null

    monochrome_logs = false
    validate_params = false
    show_hidden_params = false
    disable_ping = false
    schema_ignore_params = 'show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wfversion,wfversion_common,wf'

    wf {
        stats = true
        example_cmd = [
            "--fastq test_data/Zymo_ONT.fastq"
        ]
        common_sha = "sha91452ece4f647f62b32dac3a614635a6f0d7f8b5"
        container = "sha3208a26f28715e4a67cd4af5b4a29263343d0733"
        agent = null
    }
}

manifest {
    name            = 'treangenlab/wf-emu'
    author          = 'Treangen Lab'
    homePage        = 'https://gitlab.com/treangenlab/wf-emu'
    description     = 'Emu for EPI2ME'
    mainScript      = 'main.nf'
    nextflowVersion = '>=23.04.2'
    version       = 'v0.0.1'  // TODO: do switch to this?
}

// used by default for "standard" (docker) and singularity profiles,
// other profiles may override.
process {
    withLabel:wf_common {
        container = "ontresearch/wf-common:${params.wf.common_sha}"
    }
    withLabel:wf_metagenomics {
        container = "ontresearch/wf-metagenomics:${params.wf.container}"
    }
    withLabel:wf_emu {
        container = "docker.io/kdc10/emu:latest"
    }
    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"
        }
    }

    // using singularity instead of docker
    singularity {
        singularity {
            enabled = true
            autoMounts = true
        }
    }


    // keep stub conda profile to prevent unknown profile warning so users get a better error
    conda {
        conda.enabled = true
    }


    // Using AWS batch.
    // May need to set aws.region and aws.batch.cliPath
    awsbatch {
        process {
            executor = 'awsbatch'
            queue = "${params.aws_queue}"
            memory = '8G'
            container = "${params.aws_image_prefix}-wf-common:${params.wf.common_sha}-root"
            withLabel:wf_common {
                container = "${params.aws_image_prefix}-wf-common:${params.wf.common_sha}-root"
            }
            withLabel:wfemu {
                container = "${params.aws_image_prefix}-wf-emu:${params.wfversion}"
            }
            withLabel:wfcommon {
                container = "${params.aws_image_prefix}-wf-common:${params.wfversion_common}"
            }
            shell = ['/bin/bash', '-euo', 'pipefail']
        }
    }

    // local profile for simplified development testing
    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"
}

env {
    PYTHONNOUSERSITE = 1
}