nextflow.config

/*
 * -------------------------------------------------
 *  GEMmaker Nextflow config file
 * -------------------------------------------------
 * Default config options for all environments.
 */

params {
    pipeline = "kallisto"

    // SAMPLES
    input = null
    enable_conda = null
    skip_samples = null
    sras = null
    keep_sra = false
    keep_retrieved_fastq = false

    // KALLISTO PIPELINE
    kallisto_index_path = null
    kallisto_bootstrap_samples = 0
    kallisto_keep_data = false
    kallisto_keep_counts = true
    kallisto_keep_tpm = true
    kallisto_keep_gem = true

    // SALMON PIPELINE
    salmon_index_path = null
    salmon_keep_data = false
    salmon_keep_counts = true
    salmon_keep_tpm = true
    salmon_keep_gem = true

    // HISAT2 PIPELINE
    hisat2_base_name = null
    hisat2_index_dir = null
    hisat2_gtf_file = null
    hisat2_keep_data = false
    hisat2_keep_sam = false
    hisat2_keep_bam = false
    hisat2_keep_counts = true
    hisat2_keep_fpkm = true
    hisat2_keep_tpm = true
    hisat2_keep_gem = true

    // TRIMMOMATIC (SET FOR HISAT2 AND STAR PIPELINES)
    trimmomatic_clip_file = "${projectDir}/assets/fasta_adapter.txt"
    trimmomatic_MINLEN = 0.7
    trimmomatic_SLIDINGWINDOW = "4:15"
    trimmomatic_LEADING = 3
    trimmomatic_TRAILING = 6
    trimmomatic_keep_trimmed_fastq = false

    // STAR PIPELINE
    star_index_dir = null
    star_gtf_file = null
    star_keep_data = false
    star_keep_sam = false
    star_keep_bam = false
    star_keep_counts = true
    star_keep_fpkm = true
    star_keep_tpm = true
    star_keep_gem = true

    // Reports
    failed_run_report_template = "${projectDir}/assets/failed_sra_runs.template.html"
    multiqc_config_file = "${projectDir}/assets/multiqc_config.yaml"
    multiqc_custom_logo = "${projectDir}/assets/systemsgenetics-gemmaker_logo.png"
    publish_multiqc_report = true

    // References
    genome                     = null
    igenomes_base              = 's3://ngi-igenomes/igenomes'
    igenomes_ignore            = true

    // Boilerplate options
    outdir                     = './results'
    tracedir                   = "${params.outdir}/pipeline_info"
    publish_dir_mode           = 'link'
    email                      = null
    email_on_fail              = null
    plaintext_email            = false
    monochrome_logs            = false
    help                       = false
    validate_params            = true
    show_hidden_params         = false
    schema_ignore_params       = 'genomes,modules'
    enable_conda               = false
    singularity_pull_docker_container = false

    // Config options
    custom_config_version      = 'master'
    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    hostnames                  = [:]
    config_profile_description = null
    config_profile_contact     = null
    config_profile_url         = null
    config_profile_name        = null

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory                 = '6.GB'
    max_cpus                   = 4
    max_time                   = '72.h'
}

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

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

// Load igenomes.config if required
if (!params.igenomes_ignore) {
    includeConfig 'conf/igenomes.config'
} else {
    params.genomes = [:]
}

profiles {
    debug { process.beforeScript = 'echo $HOSTNAME' }
    conda {
        params.enable_conda    = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    docker {
        docker.enabled         = true
        docker.userEmulation   = true
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    podman {
        podman.enabled         = true
        docker.enabled         = false
        singularity.enabled    = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    shifter {
        shifter.enabled        = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        charliecloud.enabled   = false
    }
    charliecloud {
        charliecloud.enabled   = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
    }
    test      { includeConfig 'conf/test.config'      }
    test_full { includeConfig 'conf/test_full.config' }
    test_noclean { includeConfig 'conf/test_noclean.config' }
}

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.tracedir}/execution_timeline_${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}.svg"
}

manifest {
      name = 'systemsgenetics/gemmaker'
      author = 'John Hadish, Tyler Biggs, Ben Shealy, Connor Wytko, Sai Prudhvi Oruganti, F. Alex Feltus, & Stephen Ficklin'
      homePage = 'https://github.com/systemsgenetics/gemmaker'
      description = 'GEMmaker is a Nextflow workflow for large-scale gene expression sample processing, expression-level quantification and Gene Expression Matrix (GEM) construction. Results from GEMmaker are useful for differential gene expression (DGE) and gene co-expression network (GCN) analyses. The GEMmaker workflow currently supports Illumina RNA-seq datasets.'
      mainScript = 'main.nf'
      nextflowVersion = '>=21.04.0'
      version = '2.1.1'
}

// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
    if (type == 'memory') {
        try {
            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                return params.max_memory as nextflow.util.MemoryUnit
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'time') {
        try {
            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                return params.max_time as nextflow.util.Duration
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (all) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}