nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/Australian-Structural-Biology-Computing/wisps/master/nextflow_schema.json",
    "title": "Australian-Structural-Biology-Computing/wisps pipeline parameters",
    "description": "Workflow for Interaction Screening by predicting Structure",
    "type": "object",
    "$defs": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": ["input", "outdir"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_input.json",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/wisps/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "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"
                },
                "mode": {
                    "type": "string",
                    "default": "all-all",
                    "description": "Specifies the interactions to be created. You can use all-all, or group-group using teh group column in the samplesheet. You can use mu;ltiple group-group separated by a comma (',') with no spaces.",
                    "fa_icon": "fas fa-cogs",
                    "errorMessage": "Check the documenation for more details on this."
                },
                "tools": {
                    "type": "string",
                    "default": "boltz,colabfold",
                    "description": "Specifies the models to be run. tools can be any combination of ['alphafold3', 'colabfold', 'boltz'] separated by a comma (',') with no spaces.",
                    "fa_icon": "fas fa-cogs",
                    "errorMessage": "Tools must be a comma-separated list containing any combination of 'alphafold3', 'colabfold', or 'boltz' with no spaces."
                },
                "analysis_batch_size": {
                    "type": "integer",
                    "default": 20,
                    "description": "Number of samples to be processed in the analysis after multiple single alignment",
                    "fa_icon": "fas fa-microchip"
                },
                "colabfold_batch_size": {
                    "type": "integer",
                    "default": 20,
                    "description": "Number of ColabFold samples to be processed in the analysis after multiple single alignment",
                    "fa_icon": "fas fa-microchip"
                },
                "interaction_neighbours": {
                    "type": "integer",
                    "default": 0,
                    "description": "Local neighbourhood to model in all-by-all mode",
                    "fa_icon": "fas fa-microchip"
                },
                "pool": {
                    "type": "boolean",
                    "default": false,
                    "description": "Enable interaction pooling mode. When true, group pairs are read from --mode instead of standard interaction pairing.",
                    "fa_icon": "fas fa-layer-group"
                },
                "pool_size": {
                    "type": "integer",
                    "default": 2000,
                    "description": "Maximum total sequence length per interaction pool (required when --pool is set).",
                    "fa_icon": "fas fa-ruler-horizontal"
                },
                "iptm_threshold": {
                    "type": "number",
                    "default": 0,
                    "description": "Minimum iptm threshold to filter out predictions. Default is 0, and all predicitons will be ppublished in the output directory.",
                    "fa_icon": "fas fa-microchip"
                },
                "use_gpu": {
                    "type": "boolean",
                    "description": "Run on CPUs (default) or GPUs for the models",
                    "fa_icon": "fas fa-microchip"
                },
                "mmseqs_gpu": {
                    "type": "boolean",
                    "description": "Run mmseqs on CPUs (default) or GPUs",
                    "fa_icon": "fas fa-microchip"
                },
                "use_spire_db": {
                    "type": "boolean",
                    "description": "Use spire DB for search",
                    "fa_icon": "fas fa-folder-open"
                },
                "save_mmseqs_out": {
                    "type": "boolean",
                    "default": true,
                    "description": "Save the output of mmseqs in the output directory. (disable if you want to reduce storage foot print)",
                    "fa_icon": "fas fa-microchip"
                },
                "email": {
                    "type": "string",
                    "description": "Email address for completion summary.",
                    "fa_icon": "fas fa-envelope",
                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
                },
                "multiqc_title": {
                    "type": "string",
                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                    "fa_icon": "fas fa-file-signature"
                }
            }
        },
        "dbs_weights_options": {
            "title": "Databases 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": {
                "db": {
                    "type": "string",
                    "description": "Path to reference data and model parameters",
                    "fa_icon": "fas fa-folder-open"
                },
                "colabfold_uniref30": {
                    "type": "string",
                    "description": "Link to the UniRef30 database",
                    "fa_icon": "fas fa-folder-open"
                },
                "colabfold_envdb": {
                    "type": "string",
                    "description": "Link to the ColabFold database",
                    "fa_icon": "fas fa-folder-open"
                },
                "colabfold_uniref30_prefix": {
                    "type": "string",
                    "description": "Link to the ColabFold database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "colabfold_uniref30/uniref30_2302_db"
                },
                "colabfold_envdb_prefix": {
                    "type": "string",
                    "description": "Link to the ColabFold database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "colabfold_envdb/colabfold_envdb_202108_db"
                },
                "spire_db": {
                    "type": "string",
                    "description": "Link to the ColabFold database",
                    "fa_icon": "fas fa-folder-open"
                },
                "colabfold_alphafold2_params": {
                    "type": "string",
                    "description": "Link to the Alphafold2 parameters for Colabfold",
                    "fa_icon": "fas fa-folder-open"
                },
                "boltz2_aff": {
                    "type": "string",
                    "description": "Path to boltz affinity file"
                },
                "boltz2_conf": {
                    "type": "string",
                    "description": "Path to boltz-2 conf file"
                },
                "boltz2_mols": {
                    "type": "string",
                    "description": "Path to boltz-2 mols"
                },
                "alphafold3_params": {
                    "type": "string",
                    "description": "Path to Alphafold3 params"
                }
            }
        },
        "models_options": {
            "title": "Models options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Customise all parameters for the models.",
            "required": [],
            "properties": {
                "colabfold_num_recycles": {
                    "type": "integer",
                    "default": 3,
                    "description": "Number of recycles for ColabFold",
                    "fa_icon": "fas fa-recycle",
                    "minimum": 1,
                    "maximum": 20,
                    "errorMessage": "Number of recycles must be a whole number between 1 and 20"
                },
                "colabfold_search_args": {
                    "type": "string",
                    "default": null,
                    "description": "Arguments to be passed to colabfold_search",
                    "fa_icon": "fas fa-stream"
                },
                "ipsae_pae_cutoff": {
                    "type": "integer",
                    "default": 10,
                    "description": "The pae cutoff for ipsae.",
                    "fa_icon": "fas fa-recycle",
                    "errorMessage": "The pae cutoff for ipsae."
                },
                "ipsae_dist_cutoff": {
                    "type": "integer",
                    "default": 10,
                    "description": "The dist cutoff for ipsae.",
                    "fa_icon": "fas fa-recycle",
                    "errorMessage": ""
                }
            }
        },
        "institutional_config_options": {
            "title": "Institutional config options",
            "type": "object",
            "fa_icon": "fas fa-university",
            "description": "Parameters used to describe centralised config profiles. These should not be edited.",
            "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
            "properties": {
                "custom_config_version": {
                    "type": "string",
                    "description": "Git commit id for Institutional configs.",
                    "default": "master",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "custom_config_base": {
                    "type": "string",
                    "description": "Base directory for Institutional configs.",
                    "default": "https://raw.githubusercontent.com/nf-core/configs/master",
                    "hidden": true,
                    "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_name": {
                    "type": "string",
                    "description": "Institutional config name.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_description": {
                    "type": "string",
                    "description": "Institutional config description.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_contact": {
                    "type": "string",
                    "description": "Institutional config contact information.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_url": {
                    "type": "string",
                    "description": "Institutional config URL link.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                }
            }
        },
        "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": "symlink",
                    "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
                },
                "email_on_fail": {
                    "type": "string",
                    "description": "Email address for completion summary, only when pipeline fails.",
                    "fa_icon": "fas fa-exclamation-triangle",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
                    "help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
                    "hidden": true
                },
                "plaintext_email": {
                    "type": "boolean",
                    "description": "Send plain-text email instead of HTML.",
                    "fa_icon": "fas fa-remove-format",
                    "hidden": true
                },
                "max_multiqc_email_size": {
                    "type": "string",
                    "description": "File size limit when attaching MultiQC reports to summary emails.",
                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
                    "default": "25.MB",
                    "fa_icon": "fas fa-file-upload",
                    "hidden": true
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "hidden": true
                },
                "hook_url": {
                    "type": "string",
                    "description": "Incoming hook URL for messaging service",
                    "fa_icon": "fas fa-people-group",
                    "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                    "hidden": true
                },
                "multiqc_config": {
                    "type": "string",
                    "format": "file-path",
                    "description": "Custom config file to supply to MultiQC.",
                    "fa_icon": "fas fa-cog",
                    "hidden": true
                },
                "multiqc_logo": {
                    "type": "string",
                    "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
                    "fa_icon": "fas fa-image",
                    "hidden": true
                },
                "multiqc_methods_description": {
                    "type": "string",
                    "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                    "fa_icon": "fas fa-cog"
                },
                "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
                },
                "pipelines_testdata_base_path": {
                    "type": "string",
                    "fa_icon": "far fa-check-circle",
                    "description": "Base URL or local path to location of pipeline test dataset files",
                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/$defs/input_output_options"
        },
        {
            "$ref": "#/$defs/dbs_weights_options"
        },
        {
            "$ref": "#/$defs/models_options"
        },
        {
            "$ref": "#/$defs/institutional_config_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        }
    ]
}