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
    pangolin_threads = 4
    analyse_unclassified = false

    fastq = null
    sample = null
    sample_sheet = null
    min_len = null
    max_len = null
    max_softclip_length = null
    normalise = 200
    report_depth = 100
    override_basecaller_cfg = null
    scheme_name = "SARS-CoV-2"
    scheme_version = "ARTIC/V3"
    list_schemes = false
    custom_scheme = null
    genotype_variants = null
    report_clade = true
    report_lineage = true
    report_coverage = true
    report_variant_summary = true
    pangolin_options = null
    nextclade_data_tag = null
    update_data = true
    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 = 'shad28e55140f75a68f59bbecc74e880aeab16ab158'
        container_sha = 'sha21d0682f5f67b0378de70765c50f06f0aa32ecee'
        pangolin_sha = 'shae304dd3bc308a519f26908eb9d5ffa7686131d17'
        nextclade3_sha = 'sha6913f7b3db54356e74fd984933278a66b0c1f286'
    }
}

manifest {
    name            = 'epi2me-labs/wf-artic'
    author          = 'Oxford Nanopore Technologies'
    homePage        = 'https://github.com/epi2me-labs/wf-artic'
    description     = 'Run the ARTIC SARS-CoV-2 methodology on multiplexed MinION, GridION, and PromethION data.'
    mainScript      = 'main.nf'
    nextflowVersion = '>=23.04.2'
    version         = 'v1.2.2'
}

epi2melabs {
    tags = 'sars-cov-2,covid,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:${params.wf.common_sha}"
        memory = '1G'
    }
    withLabel:artic {
        container = "ontresearch/wf-artic:${params.wf.container_sha}"
        memory = '2G'
    }
    withLabel:pangolin {
        container = "ontresearch/pangolin:${params.wf.pangolin_sha}"
        memory = '2G'
    }
    withLabel:nextclade {
        container = "ontresearch/nextclade3:${params.wf.nextclade3_sha}"
        memory = '1G'
    }
    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 // for nextflow >=22.08
    }

    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:${params.wf.container_sha}"
                memory = '2G'
            }
            withLabel:pangolin {
                container = "${params.aws_image_prefix}-pangolin:${params.wf.pangolin_sha}-root"
                memory = '2G'
            }
            withLabel:nextclade {
                container = "${params.aws_image_prefix}-nextclade3:${params.wf.nextclade3_sha}"
                memory = '1G'
            }
            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"
}