params {
    // ------- Dependency Configuration --------
    // Configuration using conda is recommended for most systems.
    // Each dependency can only have one type of resource configured:
    // (Ex: bowtie2_module OR bowtie2_conda)
    
    // Dependency Configuration Using Anaconda
    // Miniconda Install Instructions:
    //     https://docs.conda.io/en/latest/miniconda.html
    //
    // -- External Conda Environments:
    facount_conda          = 'bioconda::ucsc-facount=366=*_0'
    bowtie2_conda          = 'bioconda::bowtie2=2.4.1'
    fastqc_conda           = 'bioconda::fastqc=0.11.9'
    trimmomatic_conda      = 'bioconda::trimmomatic=0.39'
    bedtools_conda         = 'bioconda::bedtools=2.29.2'
    macs2_conda            = 'bioconda::macs2=2.2.6'
    R_conda                = 'r=3.6.0'
    samtools_conda         = 'bioconda::samtools=1.9=*_11'
    bedgraphtobigwig_conda = 'libgcc-ng libpng conda-forge::libuuid mysql-connector-c openssl zlib bioconda::ucsc-bedgraphtobigwig=377'
    
    // -- Packaged/Installed Tool Conda Environments (Changes should not be necessary):
    seacr_conda         = "${params.R_conda} ${params.bedtools_conda}"
    //kseqtest_conda      = ""  // (uses binary, should not be needed)
    
    // -- Comprehensive Conda Environment (If provided, is used for all execution)
    //all_conda           = ""
    
    // Dependency Configuration Using Environment Modules
    // (values will vary depending on system)
    // To enable, comment ("//") / delete the conda-configuration and uncomment this configuration.
    // -- External Tool Modules:
    //facount_module          = ""  // Ex: "ucsc/20200320"
    //bowtie2_module          = ""  // Ex: "bowtie2/2.3.5.1"
    //fastqc_module           = ""  // Ex: "fastqc/0.11.7"
    //trimmomatic_module      = ""  // Ex: "trimmomatic/0.39"
    //bedtools_module         = ""  // Ex: "bedtools/2.29.2"
    //macs2_module            = ""  // Ex: "macs/2.2.7.1"
    //R_module                = ""  // Ex: "R/4.0"
    //bedgraphtobigwig_module = ""  // Ex: "ucsc/20200320"
    
    // -- Packaged/Installed Tool Modules (Changes should not be necessary):
    //seacr_module         = "${params.R_module}:${params.bedtools_module}"
    //kseqtest_module      = ""  // (uses binary, should not be needed)
    
    // -- Comprehensive Tool Modules (If provided, is used for all execution)
    //all_module           = ""  // Ex: "cutruntools/20200104"
    
    // System Call Settings
    //   Call executed on the system, defaults assume that each tool is available
    //     on the system PATH (as with conda setup)
    //   Can replace with direct path as desired:
    //   Ex:
    //        samtools_call = "samtools"
    //     or samtools_call = "/path/to/samtools/dir/samtools" 
    java_call             = "java"
    bowtie2_build_call    = "bowtie2-build"
    facount_call          = "faCount"
    samtools_call         = "samtools"
    fastqc_call           = "fastqc"
    trimmomatic_call      = "trimmomatic"
    bowtie2_call          = "bowtie2"
    bedtools_call         = "bedtools"
    macs2_call            = "macs2"
    bedgraphtobigwig_call = "bedGraphToBigWig"
    kseqtest_call         = "${projectDir}/CUTRUNTools/kseq_test"  //Installed with --mode initiate
    seacr_call            = "${projectDir}/SEACR/SEACR_1.3.sh"     //Packaged with download
    seacr_R_script        = "${projectDir}/SEACR/SEACR_1.3.R"      //Packaged with download
    
