nextflow.config

/*
* MIT License
*
* Copyright (c) 2022 Tobias Neumann, Daniel Malzl
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*/


/*
hicer-nf nextflow config
*/

params {

    resolutions             = ''
    genome                  = ''
    fasta                   = ''
    chromSizes              = ''
    re                      = ''
    minMapDistance          = 500
    readsPerSplit           = 25000000
    defaultResolutions      = "5000,10000,25000,50000,100000,250000,500000,1000000"
    outdir                  = 'results'
    igenomes_ignore         = false
    skip_juicer             = false
    custom_config_version   = 'master'
    custom_config_base      = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    tracedir                = "${params.outdir}/pipeline_info"

}

process.container = 'pavrilab/hicer-nf:latest'

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

// Load nf-core custom profiles from different Institutions
try {
    includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}

profiles {
    singularity {
        singularity.enabled = true
    }

    docker {
        docker.enabled      = true
    }
}

if (!params.igenomes_ignore) {
    includeConfig 'conf/igenomes.config'

} else {
    params.genomes = [:]
}

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

manifest {
    name            = 'pavrilab/hicer-nf'
    author          = 'Daniel Malzl, Tobias Neumann'
    homePage        = 'https://github.com/pavrilab/hicer-nf'
    description     = 'Hi-C data analysis pipeline'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.10.3'
    version         = '1.0.0'
}

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'