nextflow.config

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

nextflow.enable.dsl = 2

// Global defaults
params {

    // Input parameters
    run_method =            "standard"          // "standard", "geneext_only", "exteral_pipeline_only"
    mapping_software =      "starsolo"          // "starsolo", "alevin", "both"/"alevin_starsolo", "alevin_subsampled_starsolo"
    input =                 null
    outdir =                "../outdir"
    protocol =              null
    seqspec_file =          null
    bc_whitelist =          null
    bc_whitelist_parse_splitwells = null

    // References
    ref_fasta =             null
    ref_gtf =               null
    ref_gtf_alt =           null

    // Gene extension parameters
    perform_geneext =       false
    geneext_gtf =           null

    // Subsampling parameters
    subsample_nreads =      100000000

    // 10x Genomics specific parameters
    perform_10x_saturate =  true
    saturation_target =     0.7

    // Demultiplexing parameters
    perform_demultiplexing = true
    bcl2fastq =             null

    // Trimming parameters (values are set in conf/seqtech_parameters.config)
    perform_trimming =      false
    fastp_length_required = null
    fastp_qualified_quality_phred = null

    // STAR specific parameters
    star_index =            null
    star_genomeSAindexNbases = null
    star_genomeSAsparseD =  null
    star_solocellfilter =   null
    star_soloFeatures =     null
    star_outFilterScoreMin= null
    star_outSAMunmapped =   null
    star_outSAMattributes=  null
    star_soloTypestring =   null
    star_soloCBmatchWLtype= null
    star_soloUMIfiltering=  null
    star_soloMultiMappers=  null
    star_soloUMIdedup =     null
    star_clipAdapterType =  null
    star_generateBAM =      true
    star_limitBAMsortRAM =  0
    star_limitGenomeGenerateRAM = 60000000000
    star_extraargs =        null

    // Feature counting parameters
    perform_featurecounts = false
    grep_rrna =             "rRNA"
    mt_contig =             "chrM M MT"

    // Taxonomic classification parameters
    perform_kraken =        false
    kraken_db_path =        null

    // Filtering parameters
    perform_cellbender =    false
    cellbender_extraargs =  null

    // Parameters for external pipelines
    splitpipe_installation = null
    splitpipe_conda_env =   null
    splitpipe_demultiplex_script =  null
    rhapsody_installation = null
    perform_cellranger =    false

    // Boilerplate parameters
    code_dir =              null
    publish_dir_mode =      'copy'
    email =                 null
    email_on_fail =         null
    plaintext_email =       false
    hook_url =              null
    monochrome_logs =       true
    help =                  false
    help_full =             false
    version =               false
    trace_report_suffix =   new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')

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

    // Schema validation default options
    validate_params            = false
}


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


/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Define profiles for config files
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Nextflow requires the custom config files to be defined in the nextflow.config
    file as a profile, to be able to reference the params in this file.
----------------------------------------------------------------------------------------
*/
profiles {
    conda {
        conda.enabled           = true
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        conda.channels          = ['conda-forge', 'bioconda']
        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.useMicromamba     = true
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    docker {
        docker.enabled          = true
        conda.enabled           = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
        docker.runOptions       = '-u $(id -u):$(id -g)'
    }
    arm {
        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
    }
    singularity {
        singularity.enabled     = true
        singularity.autoMounts  = true
        conda.enabled           = true
        docker.enabled          = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    podman {
        podman.enabled          = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    shifter {
        shifter.enabled         = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    charliecloud {
        charliecloud.enabled    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        apptainer.enabled       = false
    }
    apptainer {
        apptainer.enabled       = true
        apptainer.autoMounts    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
    }
    wave {
        apptainer.ociAutoPull   = true
        singularity.ociAutoPull = true
        wave.enabled            = true
        wave.freeze             = true
        wave.strategy           = 'conda,container'
    }
    gitpod {
        executor.name           = 'local'
        executor.cpus           = 4
        executor.memory         = 8.GB
        process {
            resourceLimits = [
                cpus  : 2,
                memory: 4.GB,
                time  : 1.h
            ]
        }
    }
    gpu {
        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
        apptainer.runOptions    = '--nv'
        singularity.runOptions  = '--nv'
    }
}


// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
// Load nf-core/demo custom profiles from different institutions.
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/demo.config" : "/dev/null"


// Include seqtech-specific parameters
includeConfig "conf/seqtech_parameters.config"


// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry    = 'quay.io'
docker.registry       = 'quay.io'
podman.registry       = 'quay.io'
singularity.registry  = 'quay.io'
charliecloud.registry = 'quay.io'


// Manifest
manifest {
    name            = 'biodiversitycellatlas/bca_preprocessing'
    author          = 'Bonita van Waardenburg'
    homePage        = 'https://github.com/biodiversitycellatlas/bca_preprocessing'
    description     = 'Biodiversity Cell Atlas Pre-processing Pipeline'
    mainScript      = 'main.nf'
    version         = '0.2.1'
    nextflowVersion = '>=21.04.0'
}

// Nextflow plugins
plugins {
    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

validation {
    monochromeLogs = params.monochrome_logs
    help {
        enabled = true
        command = "nextflow run -profile <institution_config>,conda -c /path/to/custom_config"
        fullParameter = "help_full"
        showHiddenParameter = "show_hidden"
        beforeText = """
-\033[2m----------------------------------------------------\033[0m-
                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
                                        \033[0;32m`._,._,\'\033[0m
\033[0;35m  biodiversitycellatlas/bca_preprocessing ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
        afterText = """
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/biodiversitycellatlas/bca_preprocessing/CITATIONS.md

"""
    }
    summary {
        beforeText = validation.help.beforeText
        afterText = validation.help.afterText
    }
}