nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/proteinfold/master/nextflow_schema.json",
    "title": "nf-core/proteinfold pipeline parameters",
    "description": "Protein 3D structure prediction pipeline",
    "type": "object",
    "$defs": {
        "input_output_options": {
            "title": "Global options",
            "type": "object",
            "fa_icon": "fas fa-coins",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": ["input", "outdir"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_input.json",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "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/proteinfold/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv",
                    "errorMessage": "Input samplesheet must be a CSV file that exists. Please check the file path and format."
                },
                "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",
                    "errorMessage": "Output directory path must be specified"
                },
                "mode": {
                    "type": "string",
                    "default": "alphafold2",
                    "description": "Specifies the mode in which the pipeline will be run. mode can be any combination of ['alphafold2', 'alphafold3', 'colabfold', 'esmfold', 'rosettafold_all_atom', 'boltz', 'helixfold3', 'rosettafold2na'] separated by a comma (',') with no spaces.",
                    "fa_icon": "fas fa-cogs",
                    "pattern": "^(alphafold2|alphafold3|colabfold|esmfold|rosettafold_all_atom|helixfold3|boltz|rosettafold2na|)(,(alphafold2|alphafold3|colabfold|esmfold|rosettafold_all_atom|helixfold3|boltz|rosettafold2na)?,?)*(?<!,)$",
                    "errorMessage": "Mode must be a comma-separated list containing any combination of 'alphafold2', 'alphafold3', 'colabfold', 'esmfold', 'rosettafold_all_atom', 'boltz', or 'helixfold3' with no spaces."
                },
                "use_gpu": {
                    "type": "boolean",
                    "description": "Run on CPUs (default) or GPUs",
                    "fa_icon": "fas fa-microchip"
                },
                "save_intermediates": {
                    "type": "boolean",
                    "description": "Keep raw intermediate files",
                    "fa_icon": "fas fa-microchip"
                },
                "split_fasta": {
                    "type": "boolean",
                    "description": "Split input multi-fasta file in separated fasta files each of them containing one sequence to be folded",
                    "fa_icon": "fas fa-microchip"
                },
                "email": {
                    "type": "string",
                    "description": "Email address for completion summary.",
                    "fa_icon": "fas fa-envelope",
                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
                    "errorMessage": "Please provide a valid email address"
                },
                "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",
                    "maxLength": 100,
                    "errorMessage": "MultiQC title must be less than or equal to 100 characters"
                },
                "db": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The directory where reference data is stored. Individual methods can be overwritten with method-specific paths.",
                    "fa_icon": "fas fa-folder-open"
                },
                "full_dbs": {
                    "type": "boolean",
                    "description": "Global toggle for full database usage.",
                    "fa_icon": "fas fa-battery-full"
                },
                "uniref30_prefix": {
                    "type": "string",
                    "default": "UniRef30_2023_02",
                    "description": "UniRef major release",
                    "enum": ["UniRef30_2023_02", "UniRef30_2022_02", "UniRef30_2021_03"],
                    "fa_icon": "fas fa-database"
                },
                "use_msa_server": {
                    "type": "boolean",
                    "description": "Use the cloud MSA server",
                    "icon": "fas folder-open"
                },
                "msa_server_url": {
                    "type": "string",
                    "description": "Specify your custom MMSeqs2 API server url",
                    "fa_icon": "fas fa-link",
                    "format": "uri",
                    "errorMessage": "Please provide a valid URL for the MMSeqs2 API server"
                }
            }
        },
        "alphafold2_options": {
            "title": "AlphaFold2 options",
            "type": "object",
            "fa_icon": "fas fa-dna",
            "description": "AlphaFold2 options.",
            "properties": {
                "alphafold2_max_template_date": {
                    "type": "string",
                    "default": "2038-01-19",
                    "description": "Maximum date of the PDB templates used by 'AlphaFold2' mode",
                    "fa_icon": "fas fa-calendar-check",
                    "pattern": "^\\d{4}-\\d{2}-\\d{2}$",
                    "errorMessage": "Date must be in YYYY-MM-DD format"
                },
                "alphafold2_full_dbs": {
                    "type": "boolean",
                    "description": "If true uses the full version of the BFD database otherwise, otherwise it uses its reduced version, small bfd",
                    "fa_icon": "fas fa-battery-full"
                },
                "alphafold2_mode": {
                    "type": "string",
                    "default": "split_msa_prediction",
                    "description": "Specifies the mode in which AlphaFold2 will be run",
                    "enum": ["standard", "split_msa_prediction"],
                    "fa_icon": "fas fa-exchange-alt"
                },
                "alphafold2_model_preset": {
                    "type": "string",
                    "default": "monomer_ptm",
                    "description": "Model preset for 'AlphaFold2' mode",
                    "enum": ["monomer", "monomer_casp14", "monomer_ptm", "multimer"],
                    "fa_icon": "fas fa-stream"
                },
                "alphafold2_random_seed": {
                    "type": "integer",
                    "description": "Random seed to control stochastic alphafold inference."
                },
                "alphafold2_params_prefix": {
                    "type": "string",
                    "default": "alphafold_params_2022-12-06",
                    "description": "Alphafold2 parameters version",
                    "enum": [
                        "alphafold_params_2022-12-06",
                        "alphafold_params_2022-03-02",
                        "alphafold_params_2022-01-19",
                        "alphafold_params_2021-07-14"
                    ],
                    "fa_icon": "fas fa-database"
                }
            }
        },
        "colabfold_options": {
            "title": "ColabFold options",
            "type": "object",
            "fa_icon": "fas fa-coins",
            "description": "ColabFold options.",
            "properties": {
                "colabfold_model_preset": {
                    "type": "string",
                    "default": "alphafold2_ptm",
                    "description": "Model preset for 'colabfold' mode",
                    "enum": [
                        "alphafold2_ptm",
                        "alphafold2_multimer_v1",
                        "alphafold2_multimer_v2",
                        "alphafold2_multimer_v3"
                    ],
                    "fa_icon": "fas fa-stream"
                },
                "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_use_amber": {
                    "type": "boolean",
                    "default": true,
                    "description": "Use Amber minimization to refine the predicted structures",
                    "fa_icon": "fas fa-compress-alt"
                },
                "colabfold_use_gpu_relax": {
                    "type": "boolean",
                    "default": false,
                    "description": "Use GPU for Amber relaxation in ColabFold",
                    "fa_icon": "fas fa-microchip"
                },
                "colabfold_db_load_mode": {
                    "type": "integer",
                    "description": "Specify the way that MMSeqs2 will load the required databases in memory",
                    "fa_icon": "fas fa-download",
                    "enum": [0, 1, 2, 3],
                    "errorMessage": "DB load mode must be 0, 1, 2, or 3"
                },
                "colabfold_use_templates": {
                    "type": "boolean",
                    "default": false,
                    "description": "Use PDB templates",
                    "fa_icon": "fas fa-paste"
                },
                "colabfold_create_index": {
                    "type": "boolean",
                    "description": "Create databases indexes when running colabfold_local mode",
                    "fa_icon": "fas fa-bezier-curve"
                }
            }
        },
        "esmfold_options": {
            "title": "ESMFold options",
            "type": "object",
            "fa_icon": "fas fa-coins",
            "description": "ESMFold options.",
            "properties": {
                "esmfold_num_recycles": {
                    "type": "integer",
                    "default": 4,
                    "description": "Specifies the number of recycles used by ESMFold",
                    "fa_icon": "fas fa-server",
                    "minimum": 1,
                    "maximum": 20,
                    "errorMessage": "Number of recycles must be a whole number between 1 and 20"
                },
                "esmfold_model_preset": {
                    "type": "string",
                    "description": "Specifies whether is a 'monomer' or 'multimer' prediction",
                    "enum": ["monomer", "multimer"],
                    "fa_icon": "fas fa-stream",
                    "default": "monomer"
                }
            }
        },
        "rosettafold2na_options": {
            "title": "RosettaFold2NA options",
            "type": "object",
            "fa_icon": "fas fa-dna",
            "description": "RosettaFold2NA options.",
            "properties": {
                "rosettafold2na_db": {
                    "type": "string",
                    "format": "path",
                    "exists": true,
                    "description": "Specifies the DB and PARAMS path used by 'RosettaFold2NA' mode",
                    "fa_icon": "fas fa-database"
                }
            }
        },
        "boltz_options": {
            "title": "Boltz options",
            "type": "object",
            "fa_icon": "fas fa-database",
            "description": "Boltz options.",
            "properties": {
                "boltz_use_potentials": {
                    "type": "boolean",
                    "description": "run Boltz-2 using inference time potentials"
                },
                "boltz_use_kernels": {
                    "type": "boolean",
                    "default": true,
                    "description": "Use optimized Triton-based CUDA kernels for Boltz inference"
                },
                "boltz_model": {
                    "type": "string",
                    "description": "Sets the model to use for prediction. Default is boltz2"
                }
            }
        },
        "foldseek_options": {
            "title": "Foldseek options",
            "type": "object",
            "fa_icon": "fas fa-coins",
            "description": "Foldseek options.",
            "properties": {
                "skip_foldseek": {
                    "type": "boolean",
                    "default": true,
                    "description": "Skip foldseek structural similarity search.",
                    "fa_icon": "fas fa-fast-forward"
                },
                "foldseek_db": {
                    "type": "string",
                    "description": "The ID of Foldseek databases",
                    "fa_icon": "fas fa-server"
                },
                "foldseek_db_path": {
                    "type": "string",
                    "format": "path",
                    "exists": true,
                    "description": "Specifies the path to foldseek databases used by 'foldseek'.",
                    "fa_icon": "fas fa-folder-open"
                },
                "foldseek_easysearch_arg": {
                    "type": "string",
                    "description": "Specifies the arguments to be passed to foldseek easysearch command",
                    "fa_icon": "fas fa-server"
                }
            }
        },
        "helixfold3_options": {
            "title": "HelixFold3 options",
            "type": "object",
            "description": "HelixFold3 options",
            "default": "",
            "properties": {
                "helixfold3_precision": {
                    "type": "string",
                    "enum": ["bf16", "fp32"],
                    "description": "The numerical precision used by the HelixFold3 model.",
                    "default": "bf16"
                },
                "helixfold3_infer_times": {
                    "type": "integer",
                    "default": 4,
                    "minimum": 1,
                    "description": "Number of independent predictions made with the HelixFold3 model"
                },
                "helixfold3_max_template_date": {
                    "type": "string",
                    "default": "2038-01-19",
                    "description": "No PDB template released after this date will be used to guide predictions."
                }
            }
        },
        "process_skipping_options": {
            "title": "Process skipping options",
            "type": "object",
            "fa_icon": "fas fa-fast-forward",
            "description": "Options to skip various steps within the workflow.",
            "properties": {
                "skip_multiqc": {
                    "type": "boolean",
                    "description": "Skip MultiQC.",
                    "fa_icon": "fas fa-fast-forward"
                },
                "skip_visualisation": {
                    "type": "boolean",
                    "description": "Skip visualisation reports.",
                    "fa_icon": "fas fa-fast-forward"
                }
            }
        },
        "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"
                }
            }
        },
        "alphafold2_dbs_and_parameters_link_options": {
            "title": "AlphaFold2 DBs and parameters links options",
            "type": "object",
            "fa_icon": "fas fa-database",
            "description": "Parameters used to provide the links to the DBs and parameters public resources to AlphaFold2.",
            "properties": {
                "alphafold2_bfd_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz",
                    "description": "Link to BFD dababase",
                    "fa_icon": "fas fa-link"
                },
                "alphafold2_small_bfd_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz",
                    "description": "Link to a reduced version of the BFD dababase",
                    "fa_icon": "fas fa-link"
                },
                "alphafold2_params_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar",
                    "description": "Link to the AlphaFold2 parameters",
                    "fa_icon": "fas fa-link"
                },
                "alphafold2_mgnify_link": {
                    "type": "string",
                    "default": "https://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/2024_04/mgy_clusters.fa.gz",
                    "description": "Link to the MGnify database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold2_pdb70_link": {
                    "type": "string",
                    "default": "https://wwwuser.gwdguser.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/pdb70_from_mmcif_220313.tar.gz",
                    "description": "Link to the PDB70 database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold2_pdb_mmcif_link": {
                    "type": "string",
                    "default": "rsync.rcsb.org::ftp_data/structures/divided/mmCIF/",
                    "description": "Link to the PDB mmCIF database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold2_pdb_obsolete_link": {
                    "type": "string",
                    "default": "https://files.wwpdb.org/pub/pdb/data/status/obsolete.dat",
                    "description": "Link to the PDB obsolete database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold2_uniref30_link": {
                    "type": "string",
                    "default": "https://wwwuser.gwdguser.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz",
                    "description": "Link to the Uniclust30 database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold2_uniref90_link": {
                    "type": "string",
                    "default": "https://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz",
                    "description": "Link to the UniRef90 database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold2_pdb_seqres_link": {
                    "type": "string",
                    "default": "https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt",
                    "description": "Link to the PDB SEQRES database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold2_uniprot_sprot_link": {
                    "type": "string",
                    "default": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz",
                    "description": "Link to the SwissProt UniProt database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold2_uniprot_trembl_link": {
                    "type": "string",
                    "default": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz",
                    "description": "Link to the TrEMBL UniProt database",
                    "fa_icon": "fas fa-link"
                }
            }
        },
        "alphafold2_dbs_and_parameters_paths_options": {
            "title": "AlphaFold2 DBs and parameters paths options",
            "type": "object",
            "fa_icon": "fas fa-database",
            "description": "Parameters used to provide the paths to the DBs and parameters for AlphaFold2.",
            "properties": {
                "alphafold2_db": {
                    "type": "string",
                    "format": "path",
                    "exists": true,
                    "description": "Specifies the DB and PARAMS path used by 'AlphaFold2' mode",
                    "fa_icon": "fas fa-database",
                    "errorMessage": "Please provide a valid path to AlphaFold2 database"
                },
                "alphafold2_bfd_path": {
                    "type": "string",
                    "description": "Path to BFD dababase",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/bfd/*"
                },
                "alphafold2_small_bfd_path": {
                    "type": "string",
                    "description": "Path to a reduced version of the BFD database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/small_bfd/*"
                },
                "alphafold2_params_path": {
                    "type": "string",
                    "description": "Path to the AlphaFold2 parameters",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/params/alphafold_params_2022-12-06/*"
                },
                "alphafold2_mgnify_path": {
                    "type": "string",
                    "description": "Path to the MGnify database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/mgnify/*"
                },
                "alphafold2_pdb70_path": {
                    "type": "string",
                    "description": "Path to the PDB70 database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/pdb70/**"
                },
                "alphafold2_pdb_mmcif_path": {
                    "type": "string",
                    "description": "Path to the PDB mmCIF database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/pdb_mmcif/mmcif_files"
                },
                "alphafold2_pdb_obsolete_path": {
                    "type": "string",
                    "description": "Path to the PDB obsolete file",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/pdb_mmcif/obsolete.dat"
                },
                "alphafold2_uniref30_path": {
                    "type": "string",
                    "description": "Path to the Uniref30 database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/uniref30/*"
                },
                "alphafold2_uniref90_path": {
                    "type": "string",
                    "description": "Path to the UniRef90 database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/uniref90/*"
                },
                "alphafold2_pdb_seqres_path": {
                    "type": "string",
                    "description": "Path to the PDB SEQRES database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/pdb_seqres/*"
                },
                "alphafold2_uniprot_path": {
                    "type": "string",
                    "description": "Path to UniProt database containing the SwissProt and the TrEMBL databases",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/uniprot/*"
                }
            }
        },
        "alphafold3_dbs_and_parameters_link_options": {
            "title": "AlphaFold3 DBs and parameters links options",
            "type": "object",
            "fa_icon": "fas fa-database",
            "description": "Parameters used to provide the links to the DBs and parameters public resources to Alphafold3.",
            "properties": {
                "alphafold3_db": {
                    "type": "string",
                    "format": "path",
                    "exists": true,
                    "description": "Specifies the DB and PARAMS path used by 'AlphaFold3' mode",
                    "fa_icon": "fas fa-database",
                    "errorMessage": "Please provide a valid path to AlphaFold3 database"
                },
                "alphafold3_small_bfd_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold-databases/v3.0/bfd-first_non_consensus_sequences.fasta.zst",
                    "description": "Link to a reduced version of the BFD dababase",
                    "fa_icon": "fas fa-link"
                },
                "alphafold3_mgnify_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold-databases/v3.0/mgy_clusters_2022_05.fa.zst",
                    "description": "Link to the MGnify database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold3_pdb_mmcif_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold-databases/v3.0/pdb_2022_09_28_mmcif_files.tar.zst",
                    "description": "Link to the PDB mmCIF database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold3_uniref90_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold-databases/v3.0/uniref90_2022_05.fa.zst",
                    "description": "Link to the UniRef90 database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold3_pdb_seqres_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold-databases/v3.0/pdb_seqres_2022_09_28.fasta.zst",
                    "description": "Link to the PDB SEQRES database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold3_uniprot_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold-databases/v3.0/uniprot_all_2021_04.fa.zst",
                    "description": "Link to the UniProt database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold3_rnacentral_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold-databases/v3.0/rnacentral_active_seq_id_90_cov_80_linclust.fasta.zst",
                    "description": "Link to the RNAcentral database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold3_nt_rna_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold-databases/v3.0/nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta.zst",
                    "description": "Link to the nt_rna database",
                    "fa_icon": "fas fa-link"
                },
                "alphafold3_rfam_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold-databases/v3.0/rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta.zst",
                    "description": "Link to the Rfam database",
                    "fa_icon": "fas fa-link"
                }
            }
        },
        "alphafold3_dbs_and_parameters_path_options": {
            "title": "AlphaFold3 DBs and parameters links options",
            "type": "object",
            "fa_icon": "fas fa-database",
            "description": "Parameters used to provide the paths to the DBs and parameters for Alphafold2.",
            "properties": {
                "alphafold3_small_bfd_path": {
                    "type": "string",
                    "description": "Path to the reduced version of the BFD database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/small_bfd/*"
                },
                "alphafold3_params_path": {
                    "type": "string",
                    "description": "Path to the Alphafold3 parameters",
                    "fa_icon": "fas fa-folder-open"
                },
                "alphafold3_mgnify_path": {
                    "type": "string",
                    "description": "Path to the MGnify database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/mgnify/*"
                },
                "alphafold3_pdb_mmcif_path": {
                    "type": "string",
                    "description": "Path to the PDB mmCIF database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/pdb_mmcif/mmcif_files"
                },
                "alphafold3_uniref90_path": {
                    "type": "string",
                    "description": "Path to the UniRef90 database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/uniref90/*"
                },
                "alphafold3_pdb_seqres_path": {
                    "type": "string",
                    "description": "Path to the PDB SEQRES database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/pdb_seqres/*"
                },
                "alphafold3_uniprot_path": {
                    "type": "string",
                    "description": "Path to UniProt database containing the SwissProt and the TrEMBL databases",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/uniprot/*"
                },
                "alphafold3_rnacentral_path": {
                    "type": "string",
                    "description": "Path to the RNAcentral database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/rnacentral/*"
                },
                "alphafold3_nt_rna_path": {
                    "type": "string",
                    "description": "Path to the nt_rna database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/nt_rna/*"
                },
                "alphafold3_rfam_path": {
                    "type": "string",
                    "description": "Path to the Rfam database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/rfam/*"
                }
            }
        },
        "colabfold_dbs_and_parameters_link_options": {
            "title": "ColabFold DBs and parameters links options",
            "type": "object",
            "description": "Parameters used to provide the links to the DBs and parameters public resources to ColabFold.",
            "fa_icon": "fas fa-database",
            "properties": {
                "colabfold_db_link": {
                    "type": "string",
                    "default": "https://opendata.mmseqs.org/colabfold/colabfold_envdb_202108.db.tar.gz",
                    "description": "Link to the ColabFold database",
                    "fa_icon": "fas fa-link"
                },
                "colabfold_uniref30_link": {
                    "type": "string",
                    "default": "https://opendata.mmseqs.org/colabfold/uniref30_2302.db.tar.gz",
                    "description": "Link to the UniRef30 database",
                    "fa_icon": "fas fa-link"
                },
                "colabfold_alphafold2_params_link": {
                    "type": "string",
                    "description": "Link to the Alphafold2 parameters for Colabfold",
                    "fa_icon": "fas fa-link"
                }
            }
        },
        "colabfold_dbs_and_parameters_paths_options": {
            "title": "ColabFold DBs and parameters paths options",
            "type": "object",
            "description": "Parameters used to provide the paths to the DBs and parameters public resources to ColabFold.",
            "fa_icon": "fas fa-database",
            "properties": {
                "colabfold_db": {
                    "type": "string",
                    "format": "path",
                    "exists": true,
                    "description": "Specifies the PARAMS and DB path used by 'colabfold'  mode",
                    "fa_icon": "fas fa-folder-open",
                    "errorMessage": "Please provide a valid path to ColabFold database"
                },
                "colabfold_envdb_path": {
                    "type": "string",
                    "description": "Link to the ColabFold database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/colabfold_envdb/*"
                },
                "colabfold_uniref30_path": {
                    "type": "string",
                    "description": "Link to the UniRef30 database",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/colabfold_uniref30/*"
                },
                "colabfold_alphafold2_params_path": {
                    "type": "string",
                    "description": "Link to the Alphafold2 parameters for Colabfold",
                    "fa_icon": "fas fa-folder-open"
                },
                "colabfold_alphafold2_params_tags": {
                    "type": "object",
                    "description": "Dictionary with Alphafold2 parameters tags",
                    "fa_icon": "fas fa-stream"
                }
            }
        },
        "esmfold_parameters_link_options": {
            "title": "ESMFold parameters links options",
            "type": "object",
            "description": "Parameters used to provide the links to the parameters public resources to ESMFold.",
            "fa_icon": "fas fa-database",
            "properties": {
                "esmfold_3B_v1": {
                    "type": "string",
                    "default": "https://dl.fbaipublicfiles.com/fair-esm/models/esmfold_3B_v1.pt",
                    "description": "Link to the ESMFold 3B-v1 model",
                    "fa_icon": "fas fa-link"
                },
                "esm2_t36_3B_UR50D": {
                    "type": "string",
                    "default": "https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t36_3B_UR50D.pt",
                    "description": "Link to the ESMFold t36-3B-UR50D model",
                    "fa_icon": "fas fa-link"
                },
                "esm2_t36_3B_UR50D_contact_regression": {
                    "type": "string",
                    "default": "https://dl.fbaipublicfiles.com/fair-esm/regression/esm2_t36_3B_UR50D-contact-regression.pt",
                    "description": "Link to the ESMFold t36-3B-UR50D-contact-regression model",
                    "fa_icon": "fas fa-link"
                }
            }
        },
        "esmfold_parameters_paths_options": {
            "title": "ESMFold parameters paths options",
            "type": "object",
            "description": "Parameters used to provide the paths to the parameters public resources to ESMFold.",
            "fa_icon": "fas fa-database",
            "properties": {
                "esmfold_db": {
                    "type": "string",
                    "format": "path",
                    "exists": true,
                    "description": "Specifies the PARAMS path used by 'esmfold' mode",
                    "fa_icon": "fas fa-folder-open",
                    "errorMessage": "Please provide a valid path to ESMFold database"
                },
                "esmfold_params_path": {
                    "type": "string",
                    "description": "Link to the ESMFold parameters",
                    "fa_icon": "fas fa-folder-open",
                    "default": "null/params/*"
                }
            }
        },
        "boltz_dbs_and_model_links_options": {
            "title": "Boltz DBs and model links options",
            "type": "object",
            "fa_icon": "fas fa-database",
            "description": "Links used to provide model links and weight links to Boltz",
            "properties": {
                "boltz_ccd_link": {
                    "type": "string",
                    "description": "Link to download CCD file",
                    "icon": "fas fa-link",
                    "default": "https://huggingface.co/boltz-community/boltz-1/resolve/main/ccd.pkl"
                },
                "boltz_model_link": {
                    "type": "string",
                    "description": "Link to download model file",
                    "icon": "fas fa-link",
                    "default": "https://huggingface.co/boltz-community/boltz-1/resolve/main/boltz1_conf.ckpt"
                },
                "boltz2_aff_link": {
                    "type": "string",
                    "default": "https://huggingface.co/boltz-community/boltz-2/resolve/main/boltz2_aff.ckpt",
                    "description": "Link to download boltz affinity file"
                },
                "boltz2_conf_link": {
                    "type": "string",
                    "default": "https://huggingface.co/boltz-community/boltz-2/resolve/main/boltz2_conf.ckpt",
                    "description": "Link to download boltz-2 conf file"
                },
                "boltz2_mols_link": {
                    "type": "string",
                    "default": "https://huggingface.co/boltz-community/boltz-2/resolve/main/mols.tar",
                    "description": "Link to download boltz-2 mols"
                }
            }
        },
        "boltz_dbs_and_parameters_paths_options": {
            "title": "Boltz DBs and model paths options",
            "type": "object",
            "fa_icon": "fas fa-database",
            "description": "Paths used to provide model paths and weight paths to Boltz",
            "properties": {
                "boltz_db": {
                    "type": "string",
                    "description": "Path to boltz databases",
                    "icon": "fas folder-open"
                },
                "boltz_ccd_path": {
                    "type": "string",
                    "description": "Path to CCD file",
                    "icon": "fas folder-open",
                    "default": "null/params/ccd.pkl"
                },
                "boltz_model_path": {
                    "type": "string",
                    "description": "Path to boltz Model file",
                    "icon": "fas folder-open",
                    "default": "null/params/boltz1_conf.ckpt"
                },
                "boltz2_aff_path": {
                    "type": "string",
                    "default": "null/params/boltz2_aff.ckpt",
                    "description": "Path to boltz affinity file"
                },
                "boltz2_conf_path": {
                    "type": "string",
                    "default": "null/params/boltz2_conf.ckpt",
                    "description": "Path to boltz-2 conf file"
                },
                "boltz2_mols_path": {
                    "type": "string",
                    "default": "null/params/mols/",
                    "description": "Path to boltz-2 mols"
                }
            }
        },
        "rosettafold2na_dbs_and_parameters_link_options": {
            "title": "RosettaFold2NA DBs and parameters links options",
            "type": "object",
            "fa_icon": "fas fa-database",
            "description": "Parameters used to provide the links to the DBs and parameters public resources to RosettaFold2NA.",
            "properties": {
                "rosettafold2na_uniref30_link": {
                    "type": "string",
                    "default": "http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz"
                },
                "rosettafold2na_bfd_link": {
                    "type": "string",
                    "default": "https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz"
                },
                "rosettafold2na_pdb100_link": {
                    "type": "string",
                    "default": "https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz"
                },
                "rosettafold2na_weights_link": {
                    "type": "string",
                    "default": "https://files.ipd.uw.edu/dimaio/RF2NA_apr23.tgz"
                },
                "rfam_full_region_link": {
                    "type": "string",
                    "default": "ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.full_region.gz"
                },
                "rfam_cm_link": {
                    "type": "string",
                    "default": "ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz"
                },
                "rnacentral_rfam_annotations_link": {
                    "type": "string",
                    "default": "ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/rfam/rfam_annotations.tsv.gz"
                },
                "rnacentral_id_mapping_link": {
                    "type": "string",
                    "default": "ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/id_mapping.tsv.gz"
                },
                "rnacentral_sequences_link": {
                    "type": "string",
                    "default": "ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/sequences/rnacentral_species_specific_ids.fasta.gz"
                }
            }
        },
        "rosettafold2na_dbs_and_parameters_path_options": {
            "title": "RosettaFold2NA DBs and parameters paths options",
            "type": "object",
            "description": "Parameters used to provide the paths to the DBs and parameters for RosettaFold2NA.",
            "default": "",
            "properties": {
                "rosettafold2na_uniref30_path": {
                    "type": "string",
                    "default": "null/UniRef30_2020_06/*"
                },
                "rosettafold2na_bfd_path": {
                    "type": "string",
                    "default": "null/bfd/*"
                },
                "rosettafold2na_pdb100_path": {
                    "type": "string",
                    "default": "null/pdb100/*"
                },
                "rosettafold2na_weights_path": {
                    "type": "string",
                    "default": "null/params/network/weights/RF2NA_apr23.pt"
                },
                "rosettafold2na_rna_path": {
                    "type": "string",
                    "description": "Path to the RNA folder containing all necessary RNA databases for RF2NA",
                    "default": "null/RNA/*"
                }
            }
        },
        "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
                },
                "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,
                    "errorMessage": "File size must be specified with units (KB, MB, GB, TB)"
                },
                "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,
                    "format": "uri",
                    "errorMessage": "Please provide a valid webhook URL"
                },
                "multiqc_config": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "description": "Custom config file to supply to MultiQC.",
                    "fa_icon": "fas fa-cog",
                    "hidden": true
                },
                "multiqc_logo": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "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",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "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
                },
                "trace_report_suffix": {
                    "type": "string",
                    "fa_icon": "far calendar",
                    "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
                    "hidden": true
                },
                "help": {
                    "type": ["boolean", "string"],
                    "description": "Display the help message."
                },
                "help_full": {
                    "type": "boolean",
                    "description": "Display the full detailed help message."
                },
                "show_hidden": {
                    "type": "boolean",
                    "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
                }
            }
        },
        "rosettafold_all_atom_dbs_and_parameters_links_options": {
            "title": "RoseTTAFold All Atom DBs and parameters links options",
            "type": "object",
            "description": "Parameters used to provide the paths to the DBs and parameters for RoseTTAFold All Atom.",
            "default": "",
            "properties": {
                "rosettafold_all_atom_uniref30_link": {
                    "type": "string",
                    "default": "https://wwwuser.gwdguser.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz",
                    "description": "Link to the UniRef30 database for RoseTTAFold All Atom"
                },
                "rosettafold_all_atom_bfd_link": {
                    "type": "string",
                    "default": "https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz",
                    "description": "Link to the BFD database for RoseTTAFold All Atom"
                },
                "rosettafold_all_atom_pdb100_link": {
                    "type": "string",
                    "default": "https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz",
                    "description": "Link to the PDB100 database for RoseTTAFold All Atom"
                },
                "rosettafold_all_atom_paper_weights_link": {
                    "type": "string",
                    "default": "http://files.ipd.uw.edu/pub/RF-All-Atom/weights/RFAA_paper_weights.pt",
                    "description": "Link to the RoseTTAFold All Atom paper weights"
                }
            }
        },
        "rosettafold_all_atom_dbs_and_parameters_paths_options": {
            "title": "RoseTTAFold All Atom DBs and parameters paths options",
            "type": "object",
            "description": "Parameters used to provide the paths to the DBs and parameters for RoseTTAFold All Atom.",
            "default": "",
            "properties": {
                "rosettafold_all_atom_db": {
                    "type": "string",
                    "description": "Path to RoseTTAFold All Atom database"
                },
                "rosettafold_all_atom_uniref30_path": {
                    "type": "string",
                    "default": "null/uniref30/*",
                    "description": "Path to UniRef30 database for RoseTTAFold All Atom"
                },
                "rosettafold_all_atom_bfd_path": {
                    "type": "string",
                    "default": "null/bfd/*",
                    "description": "Path to BFD database for RoseTTAFold All Atom"
                },
                "rosettafold_all_atom_pdb100_path": {
                    "type": "string",
                    "default": "null/pdb100/*",
                    "description": "Path to PDB100 database for RoseTTAFold All Atom"
                },
                "rosettafold_all_atom_paper_weights_path": {
                    "type": "string",
                    "default": "null/params/RFAA_paper_weights.pt",
                    "description": "Path to RoseTTAFold All Atom paper weights"
                }
            }
        },
        "helixfold3_dbs_and_parameters_paths_options": {
            "title": "HelixFold3 dbs and parameters paths options",
            "type": "object",
            "description": "Parameters used to provide the paths to the DBs and parameters for HelixFold3.",
            "default": "",
            "properties": {
                "helixfold3_db": {
                    "type": "string",
                    "description": "Path to HelixFold3 database"
                },
                "helixfold3_init_models_path": {
                    "type": "string",
                    "default": "null/params/HelixFold3-240814.pdparams",
                    "description": "Path to HelixFold3 init models"
                },
                "helixfold3_uniclust30_path": {
                    "type": "string",
                    "default": "null/uniref30/*",
                    "description": "Path to UniRef30 database for HelixFold3"
                },
                "helixfold3_ccd_preprocessed_path": {
                    "type": "string",
                    "default": "null/params/ccd_preprocessed_etkdg.pkl.gz",
                    "description": "Path to CCD preprocessed file for HelixFold3"
                },
                "helixfold3_rfam_path": {
                    "type": "string",
                    "default": "null/rfam/Rfam-14.9_rep_seq.fasta",
                    "description": "Path to Rfam database for HelixFold3"
                },
                "helixfold3_bfd_path": {
                    "type": "string",
                    "default": "null/bfd/*",
                    "description": "Path to BFD database for HelixFold3"
                },
                "helixfold3_small_bfd_path": {
                    "type": "string",
                    "default": "null/small_bfd/*",
                    "description": "Path to reduced BFD database for HelixFold3"
                },
                "helixfold3_uniprot_path": {
                    "type": "string",
                    "default": "null/uniprot/*",
                    "description": "Path to UniProt database for HelixFold3"
                },
                "helixfold3_pdb_seqres_path": {
                    "type": "string",
                    "default": "null/pdb_seqres/*",
                    "description": "Path to PDB SEQRES database for HelixFold3"
                },
                "helixfold3_uniref90_path": {
                    "type": "string",
                    "default": "null/uniref90/*",
                    "description": "Path to UniRef90 database for HelixFold3"
                },
                "helixfold3_mgnify_path": {
                    "type": "string",
                    "default": "null/mgnify/*",
                    "description": "Path to MGnify database for HelixFold3"
                },
                "helixfold3_pdb_mmcif_path": {
                    "type": "string",
                    "default": "null/pdb_mmcif/mmcif_files",
                    "description": "Path to PDB mmCIF database for HelixFold3"
                },
                "helixfold3_maxit_src_path": {
                    "type": "string",
                    "default": "null/maxit-v11.200-prod-src",
                    "description": "Path to Maxit Suite for HelixFold3"
                },
                "helixfold3_obsolete_path": {
                    "type": "string",
                    "default": "null/pdb_mmcif/obsolete.dat",
                    "description": "Path to obsolete PDB file for HelixFold3"
                }
            }
        },
        "helixfold3_dbs_and_parameters_link_options": {
            "title": "HelixFold3 dbs and parameters link options",
            "type": "object",
            "description": "Parameters used to provide the links to the parameters public resources to HelixFold3.",
            "default": "",
            "properties": {
                "helixfold3_init_models_link": {
                    "type": "string",
                    "default": "https://paddlehelix.bd.bcebos.com/HelixFold3/params/HelixFold3-params-240814.zip",
                    "description": "Link to HelixFold3 init models"
                },
                "helixfold3_uniclust30_link": {
                    "type": "string",
                    "default": "https://wwwuser.gwdguser.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz",
                    "description": "Link to UniRef30 database for HelixFold3"
                },
                "helixfold3_ccd_preprocessed_link": {
                    "type": "string",
                    "default": "https://paddlehelix.bd.bcebos.com/HelixFold3/CCD/ccd_preprocessed_etkdg.pkl.gz",
                    "description": "Link to CCD preprocessed file for HelixFold3"
                },
                "helixfold3_rfam_link": {
                    "type": "string",
                    "default": "https://paddlehelix.bd.bcebos.com/HelixFold3/MSA/Rfam-14.9_rep_seq.fasta",
                    "description": "Link to Rfam database for HelixFold3"
                },
                "helixfold3_bfd_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz",
                    "description": "Link to BFD database for HelixFold3"
                },
                "helixfold3_small_bfd_link": {
                    "type": "string",
                    "default": "https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz",
                    "description": "Link to reduced BFD database for HelixFold3"
                },
                "helixfold3_pdb_seqres_link": {
                    "type": "string",
                    "default": "https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt",
                    "description": "Link to PDB SEQRES database for HelixFold3"
                },
                "helixfold3_uniref90_link": {
                    "type": "string",
                    "default": "ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz",
                    "description": "Link to UniRef90 database for HelixFold3"
                },
                "helixfold3_mgnify_link": {
                    "type": "string",
                    "default": "https://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/2024_04/mgy_clusters.fa.gz",
                    "description": "Link to MGnify database for HelixFold3"
                },
                "helixfold3_pdb_mmcif_link": {
                    "type": "string",
                    "default": "rsync.rcsb.org::ftp_data/structures/divided/mmCIF/",
                    "description": "Link to PDB mmCIF database for HelixFold3"
                },
                "helixfold3_uniprot_sprot_link": {
                    "type": "string",
                    "default": "ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz",
                    "description": "Link to UniProt SwissProt database for HelixFold3"
                },
                "helixfold3_uniprot_trembl_link": {
                    "type": "string",
                    "default": "ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz",
                    "description": "Link to UniProt TrEMBL database for HelixFold3"
                },
                "helixfold3_obsolete_link": {
                    "type": "string",
                    "default": "https://files.rcsb.org/pub/pdb/data/status/obsolete.dat",
                    "description": "Link to obsolete PDB file for HelixFold3"
                },
                "helixfold3_maxit_src_link": {
                    "type": "string",
                    "default": "https://proteinfold-dataset.s3.amazonaws.com/test-data/db/helixfold3/maxit-v11.200-prod-src.tar.gz",
                    "description": "Link to Maxit Suite for HelixFold3"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/$defs/input_output_options"
        },
        {
            "$ref": "#/$defs/alphafold2_options"
        },
        {
            "$ref": "#/$defs/colabfold_options"
        },
        {
            "$ref": "#/$defs/esmfold_options"
        },
        {
            "$ref": "#/$defs/boltz_options"
        },
        {
            "$ref": "#/$defs/foldseek_options"
        },
        {
            "$ref": "#/$defs/helixfold3_options"
        },
        {
            "$ref": "#/$defs/process_skipping_options"
        },
        {
            "$ref": "#/$defs/institutional_config_options"
        },
        {
            "$ref": "#/$defs/alphafold2_dbs_and_parameters_link_options"
        },
        {
            "$ref": "#/$defs/alphafold2_dbs_and_parameters_paths_options"
        },
        {
            "$ref": "#/$defs/alphafold3_dbs_and_parameters_link_options"
        },
        {
            "$ref": "#/$defs/alphafold3_dbs_and_parameters_path_options"
        },
        {
            "$ref": "#/$defs/colabfold_dbs_and_parameters_link_options"
        },
        {
            "$ref": "#/$defs/colabfold_dbs_and_parameters_paths_options"
        },
        {
            "$ref": "#/$defs/esmfold_parameters_link_options"
        },
        {
            "$ref": "#/$defs/esmfold_parameters_paths_options"
        },
        {
            "$ref": "#/$defs/boltz_dbs_and_model_links_options"
        },
        {
            "$ref": "#/$defs/boltz_dbs_and_parameters_paths_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        },
        {
            "$ref": "#/$defs/rosettafold_all_atom_dbs_and_parameters_links_options"
        },
        {
            "$ref": "#/$defs/rosettafold_all_atom_dbs_and_parameters_paths_options"
        },
        {
            "$ref": "#/$defs/rosettafold2na_options"
        },
        {
            "$ref": "#/$defs/rosettafold2na_dbs_and_parameters_link_options"
        },
        {
            "$ref": "#/$defs/rosettafold2na_dbs_and_parameters_path_options"
        },
        {
            "$ref": "#/$defs/helixfold3_dbs_and_parameters_link_options"
        },
        {
            "$ref": "#/$defs/helixfold3_dbs_and_parameters_paths_options"
        }
    ]
}