{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/genomeassembler/master/assets/schema_input.json",
    "title": "nf-core/genomeassembler pipeline - samplesheet schema",
    "description": "Assemble genomes from long ONT or pacbio HiFi reads",
    "type": "array",
    "items": {
        "type": "object",
        "properties": {
            "sample": {
                "type": "string",
                "pattern": "^\\S+$",
                "errorMessage": "Sample name must be provided, has to be a string value and cannot contain spaces",
                "meta": ["id"]
            },
            "ref_fasta": {
                "type": "string",
                "description": "Path to reference genome seqeunce (fasta)",
                "meta": ["ref_fasta"]
            },
            "ref_gff": {
                "type": "string",
                "description": "Path to reference genome annotations (gff)",
                "meta": ["ref_gff"]
            },
            "use_ref": {
                "type": "boolean",
                "description": "use reference genome",
                "meta": ["use_ref"]
            },
            "strategy": {
                "type": "string",
                "default": "single",
                "description": "Assembly strategy to use. Valid choices are `'single'`, `'hybrid'` and `'scaffold'`",
                "meta": ["strategy"]
            },
            "assembler": {
                "type": "string",
                "description": "Assembler to use. Valid choices depend on strategy; for single either `flye` or `hifiasm`, hybrid can be done with `hifiasm` and for scaffolded assembly provide the names of the assemblers separated with an underscore. The first assembler will be used for ONT reads, the second for HiFi reads. (see below, asembler1 and assembler_hifi)",
                "enum": ["flye", "hifiasm", "flye_hifiasm", "hifiasm_hifiasm", "flye_flye", "hifiasm_flye"],
                "default": "hifiasm",
                "meta": ["assembler"]
            },
            "assembly_scaffolding_order": {
                "type": "string",
                "default": "ont_on_hifi",
                "description": "When strategy is \"scaffold\", which assembly should be scaffolded onto which?",
                "enum": ["ont_on_hifi", "hifi_on_ont"],
                "meta": ["assembly_scaffolding_order"]
            },
            "genome_size": {
                "type": "string",
                "description": "expected genome size, optional",
                "meta": ["genome_size"]
            },
            "flye_mode": {
                "type": "string",
                "description": "flye mode",
                "default": "--nano-hq",
                "enum": ["--pacbio-raw", "--pacbio-corr", "--pacbio-hifi", "--nano-raw", "--nano-corr", "--nano-hq"],
                "meta": ["flye_mode"]
            },
            "flye_args": {
                "type": "string",
                "description": "additional args for flye",
                "meta": ["flye_args"]
            },
            "hifiasm_args": {
                "type": "string",
                "description": "Extra arguments passed to `hifiasm`",
                "meta": ["hifiasm_args"]
            },
            "assembler_ont": {
                "type": "string",
                "description": "assembler_ont assembles ONT reads. This option is mainly useful when building more complex samplesheets",
                "meta": ["assembler_ont"]
            },
            "assembler_ont_args": {
                "type": "string",
                "description": "Arguments to be passed to assembler_ont (ONT)",
                "meta": ["assembler_ont_args"]
            },
            "assembler_hifi": {
                "type": "string",
                "description": "assembler_hifi assembles HiFi reads. This option is mainly useful when building more complex samplesheets",
                "meta": ["assembler_hifi"]
            },
            "assembler_hifi_args": {
                "type": "string",
                "description": "Arguments to be passed to assembler_hifi (HiFi)",
                "meta": ["assembler_hifi_args"]
            },
            "ontreads": {
                "type": "string",
                "description": "Path to ONT reads",
                "meta": ["ontreads"]
            },
            "ont_collect": {
                "type": "boolean",
                "description": "Collect ONT reads from several files?",
                "meta": ["ont_collect"]
            },
            "ont_adapters": {
                "type": "string",
                "description": "Adaptors for ONT read-trimming",
                "meta": ["ont_adapters"]
            },
            "ont_fastplong_args": {
                "type": "string",
                "description": "Additional args to be passed to fastplong for ONT reads",
                "meta": ["ont_fastplong_args"]
            },
            "hifireads": {
                "type": "string",
                "description": "Path to HiFi reads",
                "meta": ["hifireads"]
            },
            "hifi_adapters": {
                "type": "string",
                "description": "Adaptors for HiFi read-trimming",
                "meta": ["hifi_adapters"]
            },
            "hifi_fastplong_args": {
                "type": "string",
                "description": "Additional args to be passed to fastplong for HiFi reads",
                "meta": ["hifi_fastplong_args"]
            },
            "jellyfish": {
                "type": "boolean",
                "description": "Run jellyfish and genomescope (recommended)",
                "meta": ["jellyfish"]
            },
            "jellyfish_k": {
                "type": "integer",
                "default": 21,
                "description": "Value of k used during k-mer analysis with jellyfish",
                "meta": ["jellyfish_k"]
            },
            "jellyfish_size": {
                "type": "string",
                "default": "200M",
                "description": "Initial hash size used by jellyfish count",
                "meta": ["jellyfish_size"]
            },
            "polish_pilon": {
                "type": "boolean",
                "description": "Polish assembly with pilon? Requires short reads",
                "meta": ["polish_pilon"]
                },
            "polish_dorado": {
                "type": "boolean",
                "description": "Polish assembly with dorado (ONT only)",
                "meta": ["polish_dorado"]
            },
            "polish_medaka": {
                "type": "boolean",
                "description": "Polish assembly with medaka (ONT only)",
                "meta": ["polish_medaka"]
            },
            "medaka_model": {
                "type": "string",
                "description": "model to use with medaka",
                "meta": ["medaka_model"]
            },
            "scaffold_longstitch": {
                "type": "boolean",
                "description": "Scaffold with longstitch?",
                "meta": ["scaffold_longstitch"]
            },
            "scaffold_links": {
                "type": "boolean",
                "description": "Scaffolding with links?",
                "meta": ["scaffold_links"]
            },
            "scaffold_ragtag": {
                "type": "boolean",
                "description": "Scaffold with ragtag (requires reference)?",
                "meta": ["scaffold_ragtag"]
            },
            "scaffold_hic": {
                "type": "boolean",
                "description": "Scaffold using HiC reads using yahs (requires reads)?",
                "meta": ["scaffold_hic"]
            },
            "hic_aligner": {
                "type": "string",
                "enum": ["bwa-mem2", "minimap2"],
                "description": "Aligner to use for HiC reads; default: bwa-mem2",
                "default": "bwa-mem2",
                "meta": ["hic_aligner"]
            },
            "merqury": {
                "type": "boolean",
                "default": false,
                "description": "Run merqury (if short reads are provided)",
                "meta": ["merqury"]
            },
            "qc_reads": {
                "type": "string",
                "description": "Long reads that should be used for QC when both ONT and HiFi reads are provided. Options are `'ont'` or `'hifi'`",
                "enum": ["ont", "hifi"],
                "default": "ont",
                "meta": ["qc_reads"]
            },
            "busco": {
                "type": "boolean",
                "description": "Run BUSCO?",
                "meta": ["busco"]
            },
            "busco_db": {
                "type": "string",
                "format": "directory-path",
                "description": "Path to busco db (optional)",
                "meta": ["busco_db"]
            },
            "busco_lineage": {
                "type": "string",
                "description": "Busco lineage to use",
                "default": "auto_euk",
                "meta": ["busco_lineage"]
            },
            "quast": {
                "type": "boolean",
                "description": "Run quast",
                "meta": ["quast"]
            },
            "ref_map_bam": {
                "type": "string",
                "format": "file-path",
                "description": "A mapping (bam) of reads mapped to the reference can be provided for QC. If provided, alignment to reference fasta will not run.",
                "meta": ["ref_map_bam"]
            },
            "assembly": {
                "type": "string",
                "description": "Can be used to proved existing assembly will skip assembly and perform downstream steps including qc",
                "meta": ["assembly"]
            },
            "assembly_map_bam": {
                "type": "string",
                "format": "file-path",
                "description": "A mapping (bam) of reads mapped to the provided assembly can be specified for QC. If provided, alignment to the provided assembly fasta will not run",
                "meta": ["assembly_map_bam"]
            },
            "csi_index_size": {
                "type": "integer",
                "description": "Index size to use for csi index (default: 14), creating and index of size 2^csi_index_size. See samtools index documentation for details. ",
                "default": 14,
                "meta": ["csi_index_size"]
            },
            "lift_annotations": {
                "type": "boolean",
                "description": "Lift-over annotations (requires ref_gff)?",
                "default": false,
                "meta": ["lift_annotations"]
            },
             "use_short_reads": {
                "type": "boolean",
                "description": "Use short reads?",
                "meta": ["use_short_reads"]
            },
            "shortread_trim": {
                "type": "boolean",
                "description": "Trim short reads?",
                "meta": ["shortread_trim"]
            },
            "meryl_k": {
                "type": "integer",
                "description": "kmer length for meryl / merqury",
                "default": 21,
                "minimum": 1,
                "meta": ["meryl_k"]
            },
            "shortread_F": {
                "type": "string",
                "format": "file-path",
                "description": "Path to forward short reads",
                "meta": ["shortread_F"]
            },
            "shortread_R": {
                "type": "string",
                "format": "file-path",
                "description": "Path to reverse short reads",
                "meta": ["shortread_R"]
            },
            "paired": {
                "type": "boolean",
                "description": "Are shortreads paired?",
                "meta": ["paired"]
            },
            "hic_trim": {
                "type": "boolean",
                "description": "Trim HiC short reads?",
                "default": false,
                "meta": ["hic_trim"]
            },
            "hic_F": {
                "type": "string",
                "format": "file-path",
                "description": "Path to forward HiC short reads",
                "meta": ["hic_F"]
            },
            "hic_R": {
                "type": "string",
                "format": "file-path",
                "description": "Path to reverse HiC short reads",
                "meta": ["hic_trim"]
            }
        },
        "required": ["sample"]
    }
}