EM-seq/nextflow.config at master · nebiolabs/EM-seq · GitHub

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

// Global default params, used in configs
params {
    email                     = 'undefined'
    flowcell                  = 'undefined'
    ubam_dir                  = './'
    workflow                  = 'EM-seq'
    outputDir                 = "em-seq_output"
    tmp_dir                   = '/tmp'
    fastq_split_lines         = 8000000 // approx 4M reads
    enable_neb_agg            = false
    skip_target_bed           = false
    target_bed_slop           = 50
    methyl_quality_threshold  = 20
    single_end                = false

    // NEB only
    path_to_ngs_agg           = null
    workflow_name_modifier    = null

}

includeConfig 'conf/base.config'
includeConfig 'conf/references.config'

profiles {
    debug {
        dumpHashes             = true
        process.beforeScript   = 'echo $HOSTNAME'
        cleanup                = false
    }
    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
    }
    micromamba {
        conda.enabled          = true
        conda.useMamba         = false
        conda.useMicromamba    = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }

    test {
        includeConfig 'conf/test.config'
        conda.enabled          = true
        conda.useMicromamba    = true
        conda.cacheDir         = "${projectDir}/.conda/envs"
    }
}

env {
    PYTHONNOUSERSITE = 1
}

executor {
    name = 'sge'
    queueSize = 10000
    jobName = { "${task.process.tokenize(':')[-1]}" }
}

process.shell = ['/bin/bash', '-euo', 'pipefail']

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.outputDir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file    = "${params.outputDir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.outputDir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
    enabled = true
    file    = "${params.outputDir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}