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
    sequencing_summary_source = null
    barcoding_summary_pass = null
    barcoding_summary_fail = null
    telemetry_source = null
    fast5_source = null
    bam_source = null
    fastq_source = null
    barcoding = false
    barcodes = null
    report_name = 'ToulligQC_report'
    out_dir = "output"
    sample = null
    sample_sheet = null
    aws_image_prefix = null
    aws_queue = null
    disable_ping = false
    analyse_unclassified = false
    process_label = "wfqc"
    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 {
        fastcat_stats = false
        example_cmd = [
            "--input_files 'sequencing_summary + telemetry_source'",
            "--sequencing_summary_source 'demo_data/sequencing_summary.txt'",
            "--telemetry_source 'demo_data/sequencing_telemetry.js'"
        ]
        //container_sha = "shaee16e78afd054a8cec95a293277f113abba597e5"
        container_sha = "2.7"
        agent = null
    }
}

manifest {
    name            = 'genomiqueens/wf-toulligqc'
    author          = 'GenomiqueENS'
    homePage        = 'https://github.com/GenomiqueENS/wf-toulligqc'
    description     = 'A post sequencing QC tool for Oxford Nanopore sequencers'
    mainScript      = 'main.nf'
    nextflowVersion = '>=20.10.0'
    version         = 'v1.2'
}

executor {
    $local {
        cpus = 4
        memory = "8 GB"
    }
}


// used by default for "standard" (docker) and singularity profiles,
// other profiles may override.
process {
    withLabel:wfqc {
        //container = "ontresearch/wf-template:${params.wf.container_sha}"
        container = "genomicpariscentre/wf-toulligqc:${params.wf.container_sha}"
    }
    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
    }



    // 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
}