{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/phyloplace/master/assets/schema_input.json",
    "title": "nf-core/phyloplace pipeline - params.input schema",
    "description": "Schema for the file provided with params.input",
    "type": "array",
    "items": {
        "type": "object",
        "properties": {
            "sample": {
                "type": "string",
                "pattern": "^\\S+$",
                "errorMessage": "Sample name must be provided and cannot contain spaces"
            },
            "queryfile": {
                "type": "string",
                "pattern": "^\\S+$",
                "errorMessage": "File with query sequences to place in phylogeny. Any format supported by hmmaling in HMMER (e.g. fasta, clustal, phylip, stockholm)."
            },
            "refalignment": {
                "type": "string",
                "pattern": "^\\S+$",
                "errorMessage": "Multiple sequence alignment of reference sequences. Any format suppored by hmmbuild in HMMER (see queryfile for examples)."
            },
            "refphylogeny": {
                "type": "string",
                "pattern": "^\\S+$",
                "errorMessage": "Newick formatted file with the reference phylogeny."
            },
            "hmmfile": {
                "type": "string",
                "pattern": "^\\S+$",
                "errorMessage": "HMM file to use for alignment, if the reference sequences are not aligned."
            },
            "model": {
                "type": "string",
                "pattern": "^\\S+$",
                "errorMessage": "Phylogenetic model to use in placement, see EPA-NG documentation."
            },
            "alignmethod": {
                "type": "string",
                "pattern": "^\\S+$",
                "errorMessage": "Method to use for aligning: 'hmmer' or 'mafft'."
            }
        },
        "required": ["sample", "queryfile", "refalignment", "refphylogeny", "model"]
    }
}
