nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/seqeralabs/nf-chai/master/nextflow_schema.json",
    "title": "seqeralabs/nf-chai pipeline parameters",
    "description": "Nextflow pipeline to run the Chai-1, SOTA model for biomolecular structure prediction",
    "type": "object",
    "$defs": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": ["input", "outdir"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.(fa|fasta)$",
                    "description": "Path to input FASTA file containing the sequence(s) to predict.",
                    "help_text": "The input FASTA file should contain one or more sequences in standard FASTA format.",
                    "fa_icon": "fas fa-dna"
                },
                "outdir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                    "fa_icon": "fas fa-folder-open"
                },
                "weights_dir": {
                    "type": "string",
                    "format": "directory-path",
                    "exists": true,
                    "description": "Directory containing model weights and other artifacts required by Chai-1.",
                    "fa_icon": "fas fa-folder-open"
                },
                "msa_dir": {
                    "type": "string",
                    "format": "directory-path",
                    "exists": true,
                    "description": "Directory containing precomputed multiple-sequence alignments",
                    "fa_icon": "fas fa-align-justify"
                },
                "use_gpus": {
                    "type": "boolean",
                    "description": "Run compatible tasks on GPUs rather than CPUs (default).",
                    "fa_icon": "fas fa-microchip"
                },
                "num_trunk_recycles": {
                    "type": "integer",
                    "default": 3,
                    "fa_icon": "fas fa-recycle",
                    "description": "Number of trunk recycles",
                    "hidden": true
                },
                "num_diffusion_timesteps": {
                    "type": "integer",
                    "default": 200,
                    "fa_icon": "fas fa-shoe-prints",
                    "hidden": true,
                    "description": "Number of diffusion steps to use."
                },
                "seed": {
                    "type": "integer",
                    "default": 42,
                    "fa_icon": "fas fa-seedling",
                    "hidden": true,
                    "description": "Random seed to be used for Chai-1 calculations"
                },
                "use_esm_embeddings": {
                    "type": "boolean",
                    "default": true,
                    "fa_icon": "fas fa-stamp",
                    "hidden": true,
                    "description": "Use user-provided esm model embeddings"
                }
            }
        },
        "generic_options": {
            "title": "Generic options",
            "type": "object",
            "fa_icon": "fas fa-file-import",
            "description": "Less common options for the pipeline, typically set in a config file.",
            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
            "properties": {
                "version": {
                    "type": "boolean",
                    "description": "Display version and exit.",
                    "fa_icon": "fas fa-question-circle",
                    "hidden": true
                },
                "publish_dir_mode": {
                    "type": "string",
                    "default": "copy",
                    "description": "Method used to save pipeline results to output directory.",
                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                    "fa_icon": "fas fa-copy",
                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                    "hidden": true
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "hidden": true
                },
                "validate_params": {
                    "type": "boolean",
                    "description": "Boolean whether to validate parameters against the schema at runtime",
                    "default": true,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/$defs/input_output_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        }
    ]
}