nextflow.config

params {

	// a help parameter for print all the available parameters.
	help                 = null

	/*
    a bed file of primer coordinates relative to the reference provided with the
    parameters `refseq` and `ref_gbk`.
    */
	primer_bed           = null

	// suffixes in the primer bed file denoting whether a primer is forward or reverse
	fwd_suffix           = "_LEFT"
	rev_suffix           = "_RIGHT"

	// The reference sequence to be used for mapping in FASTA format.
	refseq               = null

	// The reference sequence to be used for variant annotation in Genbank format.
	ref_gbk              = null

	// A tsv file of primer sequences
	primer_tsv           = null

	/*
    A remote location to use with a ssh client to watch for pod5 files in
    realtime as they are generated by the sequencing instrument.
    */
	remote_pod5_location = ""

	/*
    Configuration file for remote file monitoring. An example can be found at
    conf/file_watcher.template.yml
    */
	file_watcher_config  = ""

	// where to cache pod5s as they arrive from the remote location
	pod5_staging         = "${launchDir}/pod5_cache"

	/* If a remote pod5 location isn't given, users may provide a local,
    on-device directory where pod5 files have been manually transferred.
    */
	pod5_dir             = ""

	/*
    A local directory to watch for Nanopore FASTQs or BAMs as the become
    available. This is for cases where basecalling is being performed via another
    workflow, resulting in BAMs or FASTQs that are gradually transferred into
    `params.precalled_staging` as basecalling completes.
    */
	precalled_staging    = ""

	/*
    If pod5 files have already been basecalled and demultiplexed, users can
    specify their location with prepped data.
    */
	prepped_data         = ""

	/*
    If users have Illumina data to be processed, they may specify their
    paired-end FASTQ files' location with `illumina_fastq_dir`.
    */
	illumina_fastq_dir   = ""

	/*
    the Nanopore basecalling model to apply to the provided pod5 data (defaults
    to the latest super-accuracy version)
    */
	model                = "sup@latest"

	/*
    where to cache the models locally (defaults to a directory called models/
    that will be placed alongside the other workflow files). Models will only be
    downloaded upon the user's first execution of the workflow unless the user
    deletes the models directory.
    */
	model_cache          = "${launchDir}/work/basecalling_models"

	// The Nanopore barcoding kit used to prepare sequencing libraries.
	kit                  = null

	/*
    How many pod5 files to basecall at once. With a single available GPU, all
    pod5 files should be basecalled together, so this parameter defaults to
    telling Nextflow to take all pod5 files at once.
    */
	pod5_batch_size      = null

	/*
    If basecalling pod5 files is to be parallelized across multiple available
    GPUs, this parameter tells Nextflow how many parallel instances of the
    basecaller to run at once (defaults to 1).
    */
	basecall_max         = 1

	// the maximum acceptable length for a given read
	max_len              = 12345678910

	// the minimum acceptable length for a given read
	min_len              = 1

	// the minimum acceptable average quality for a given read
	min_qual             = 20

	/*
    Whether to turn on secondary alignments for each amplicon. Secondary alignments can
    increase depth at the cost of more reads potentially mapping to the wrong locations.
    By default, secondary alignments are off.
    */
	secondary            = null

	/*
    The maximum number of mismatches to allow when finding primers (defaults
    to 0)
    */
	max_mismatch         = 0

	/*
	Limit forward primer search to the first N bases of each read. This is a
	performance optimization for long reads (e.g., Nanopore) where primers are
	expected near read termini. Set to 0 (default) to search the entire read.
	*/
	forward_window       = 0

	/*
	Limit reverse primer search to the last N bases of each read. This is a
	performance optimization for long reads (e.g., Nanopore) where primers are
	expected near read termini. Set to 0 (default) to search the entire read.
	*/
	reverse_window       = 0

	/*
	Disable primer trimming. When set to true, amplicons are identified by their
	primer sequences but the primers are not trimmed from the output. This is useful
	when you want to identify which reads contain valid amplicons without modifying
	the sequences.
	*/
	no_primer_trim       = null

	// Desired coverage to downsample to, with a sentinal value of 0 to indicate 0 downsampling
	downsample_to        = 0

	// Early downsampling param
	early_downsample_to  = 0

	/*
    The minimum required frequency of a variant base to be included in a consensus
    sequence.
    */
	min_consensus_freq   = 0.5

	// The minimum required read support to report an amplicon-haplotype
	min_haplo_reads      = 2

	// deduplication flag, by default false 
	dedup                = null

	/*
    Where to cache a custom snpEff database (defaults to a directory called
    snpEff_cache/ that will be placed alongside the other workflow files). Like
    with the model data, this database will only be generated upon the user's
    first execution of the workflow unless the user deletes the snpEff_cache
    directory
    */
	snpeff_cache         = "${launchDir}/work/snpEff_cache"

	// Minimum depth of coverage
	min_depth_coverage   = 10

	// nextclade dataset
	nextclade_dataset    = null

	// Dataset, either a local FASTA file or a pre-built dataset built by Sylph, to use
	// for metagenomic profiling
	meta_ref             = null

	// for identifying sylph tax database
	sylph_tax_db         = null
	sylph_db_link        = null

	// Contamination FASTA dataset to scrub from reads
	contam_fasta         = null
	contam_link          = null

	// K-mer size to use for metagenomic sketching
	k                    = 31

	// devider haplotype phasing preset
	devider_preset       = "nanopore-r10"
	// old-long-reads, nanopore-r9, nanopore-r10, hi-fi

	// nextclade dataset cache
	nextclade_cache      = "${launchDir}/work/nextclade_datasets"

	//launch dir
	launch_dir           = "${launchDir}"

	// Whether to plot multisample coverages with a log scale
	log                  = null

	// Where to place results
	results              = "${launchDir}/results"

	// Whether to run in low-memory mode, which limits the number of parallel instances
	// of high-memory files
	low_memory           = null

	// whether to cleanup work directory after a successful run (defaults to false)
	cleanup              = null


	// where test results should go, default test
	// test = "test"


	// parameters that generally should not be overwritten in normal use cases
	// ---------------------------------------------------------------------- //

	// snpEff config file
	snpEff_config        = "${projectDir}/conf/snpeff.config"

	// email address to notify on completion. Multiple comma dilimeted emails may be provided.
	email                = null
}

// load platform-specific configurations
includeConfig params.remote_pod5_location != "" || params.pod5_dir != "" || params.precalled_staging || params.prepped_data
	? "conf/nanopore.config"
	: "conf/illumina.config"

// load reporting configuration (applies to both platforms)
includeConfig "conf/reporting.config"


// WHETHER TO GENERATE A REPORT OF RUN STATISTICS
report {
	enabled   = true
	overwrite = true
	file      = "${params.results}/report.html"
}


// WHETHER TO GENERATE A VISUALIZATION OF THE WORKFLOW
dag {
	enabled   = true
	overwrite = true
	file      = "${params.results}/workflow-visualization.png"
}


// WHETHER TO REMOVE TEMPORARY FILES AFTER A SUCCESSFUL RUN
cleanup = params.cleanup


// PROFILE OPTIONS
profiles {

	standard {

		docker.enabled      = true
		singularity.enabled = false
		conda.enabled       = false

		process.container   = "nrminor/oneroof:2.2.1"
	}

	docker {

		docker.enabled      = true
		singularity.enabled = false
		conda.enabled       = false

		process.container   = "nrminor/oneroof:2.2.1"
	}

	singularity {

		singularity.enabled = true
		docker.enabled      = false
		conda.enabled       = false

		process.container   = "docker://nrminor/oneroof:2.2.1"
	}

	apptainer {

		apptainer.enabled = true
		docker.enabled    = false
		conda.enabled     = false

		process.container = "docker://nrminor/dorado-and-friends:v0.2.3"
	}

	containerless {

		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false
	}

	// =========================================================================
	// PRESET PROFILES
	// These configure databases for specific analysis types. Combine with
	// execution profiles above, e.g.: -profile virus,docker
	// =========================================================================

	virus {
		// General viral metagenomics: IMG/VR 4.1 + panhuman decontamination
		includeConfig "conf/presets/virus.config"
	}

	sarscov2 {
		// SARS-CoV-2 analysis: virus preset + Nextclade dataset
		includeConfig "conf/presets/sarscov2.config"
	}

	// =========================================================================
	// TEST PROFILES
	// =========================================================================

	// illumina tests 
	illumina_test_with_primers {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/illumina_tests/illumina_with_primers_test.config"
	}

	illumina_test_without_primers {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/illumina_tests/illumina_without_primers_test.config"
	}

	illumina_test_with_metagenomics {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/illumina_tests/illumina_with_metagenomics.config"
	}

	illumina_test_with_phylo {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/illumina_tests/illumina_with_phylo_test.config"
	}

	illumina_test_missing_fastq {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/illumina_tests/illumina_missing_fastq.config"
	}

	illumina_test_bad_primers {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/illumina_tests/illumina_bad_primer_input.config"
	}

	illumina_test_decon {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/illumina_tests/illumina_decontaminate_test.config"
	}

	// nanopore tests 

	nanopore_test_with_primers {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/nanopore.config"
		includeConfig "conf/nanopore_tests/nanopore_with_primers_test.config"
	}

	nanopore_test_without_primers {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/nanopore.config"
		includeConfig "conf/nanopore_tests/nanopore_without_primers_test.config"
	}

	nanopore_test_with_haplo {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/nanopore.config"
		includeConfig "conf/nanopore_tests/nanopore_with_haplotyping.config"
	}

	nanopore_test_with_metagenomics {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/nanopore.config"
		includeConfig "conf/nanopore_tests/nanopore_with_metagenomics.config"
	}

	nanopore_test_with_phylo {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/nanopore.config"
		includeConfig "conf/nanopore_tests/nanopore_with_phylo_test.config"
	}

	nanopore_test_missing_input {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/nanopore.config"
		includeConfig "conf/nanopore_tests/nanopore_no_input_data.config"
	}

	nanopore_test_bad_primers {
		apptainer.enabled = false
		docker.enabled    = false
		conda.enabled     = false

		includeConfig "conf/nanopore.config"
		includeConfig "conf/nanopore_tests/nanopore_bad_primers.config"
	}
}


// MANIFEST
manifest {
	name          = "oneroof"
	homePage      = 'https://github.com/nrminor/oneroof'
	mainScript    = 'main.nf'
	defaultBranch = 'main'
	description   = 'Base-, Variant-, and Consensus-calling under One Proverbial Roof.'
	author        = 'Nicholas R. Minor'
}