nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/socialgene/sgnf/master/nextflow_schema.json",
    "title": "socialgene/sgnf pipeline parameters",
    "description": "Scalable genome mining with SocialGene knowledge graphs",
    "type": "object",
    "definitions": {
        "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": [],
            "properties": {
            "genbank_csv": {
                "type": "string",
                "mimetype": "text/csv",
                "format": "file-path-pattern",
                "exists": true,
                "description": "Additional input CSV samplesheet containing information about pre-computed assemblies. When set, both read pre-processing and assembly are skipped and the pipeline begins at the binning stage.",
                "help_text": "If you have pre-computed assemblies from another source, it is possible to jump straight to the binning stage of the pipeline by supplying these assemblies in a CSV file. This CSV file should have at minimum three columns and the following header: `id,group,assembler,fasta` (group is only required when `--coassemble_group). Short reads must still be supplied in to `--input` in CSV format. See [usage docs](https://nf-co.re/mag/usage#input-specifications) for further details.",
                "fa_icon": "fas fa-file-csv"
            },
            "fasta_csv": {
                "type": "string",
                "mimetype": "text/csv",
                "format": "file-path-pattern",
                "exists": true,
                "description": "Additional input CSV samplesheet containing information about pre-computed assemblies. When set, both read pre-processing and assembly are skipped and the pipeline begins at the binning stage.",
                "help_text": "If you have pre-computed assemblies from another source, it is possible to jump straight to the binning stage of the pipeline by supplying these assemblies in a CSV file. This CSV file should have at minimum three columns and the following header: `id,group,assembler,fasta` (group is only required when `--coassemble_group). Short reads must still be supplied in to `--input` in CSV format. See [usage docs](https://nf-co.re/mag/usage#input-specifications) for further details.",
                "fa_icon": "fas fa-file-csv"
            },
            "fna_csv": {
                "type": "string",
                "mimetype": "text/csv",
                "format": "file-path-pattern",
                "exists": true,
                "description": "Additional input CSV samplesheet containing information about pre-computed assemblies. When set, both read pre-processing and assembly are skipped and the pipeline begins at the binning stage.",
                "help_text": "If you have pre-computed assemblies from another source, it is possible to jump straight to the binning stage of the pipeline by supplying these assemblies in a CSV file. This CSV file should have at minimum three columns and the following header: `id,group,assembler,fasta` (group is only required when `--coassemble_group). Short reads must still be supplied in to `--input` in CSV format. See [usage docs](https://nf-co.re/mag/usage#input-specifications) for further details.",
                "fa_icon": "fas fa-file-csv"
            }
        }},
        "input_genomes": {
            "title": "Input Genomes",
            "type": "object",
            "description": "Any one or more of the following can be used to download/input genomes for the pipeline",
            "default": "",
            "properties": {
                "ncbi_genome_download_command": {
                    "type": "string",
                    "description": "Arguments to pass to ncbi_genome_download_command",
                    "help_text": "See the following link for more info about commands you can use:\nhttps://github.com/kblin/ncbi-genome-download"
                },
                "ncbi_datasets_command": {
                    "type": "string",
                    "description": "Taxonomic name  (maybe NCBI taxonomy id as well?) see extended help before using",
                    "help_text": "Note/Warning: \nSpecifying a taxon directly has the potential to download a large number of genomes that you may not be prepared to handle.\nI highly recommend searching here (https://www.ncbi.nlm.nih.gov/genome/browse#!/prokaryotes/) first to get an idea of how many input genomes you can expect.\n\n\nThe input argument you provide s replace the `$params.ncbi_datasets_command` in the command below:\n\n`datasets download $params.ncbi_datasets_command --dehydrated $args`\n\nThe value of `$args` is set in https://github.com/socialgene/sgnf/blob/main/conf/modules.config\n\nInfo on use of NCBI datasets can be found here: https://www.ncbi.nlm.nih.gov/datasets/docs/v1/reference-docs/command-line/datasets/"
                },
                "ncbi_datasets_file": {
                    "type": "string",
                    "description": "Instead of using the 'ncbi_datasets_command', the path to a file of NCBI genome accessions to download can provided (single accessio per line)"
                },
                "local_genbank": {
                    "type": "string",
                    "description": "Path to local GenBank file(s), can be a glob",
                    "help_text": "Accepted files:\ngbff, gbk\nand gzipped versions of those\n"
                },
                "local_faa": {
                    "type": "string",
                    "description": "Path to local protein FASTA file(s), can be a glob"
                },
                "local_fna": {
                    "type": "string",
                    "description": "Path to local assemblies in nucleotide format (to be annotated with Prokka)"
                },
                "paired_omics_json_path": {
                    "type": "string",
                    "description": "Paired omics json file, downloaded from: https://pairedomicsdata.bioinformatics.nl/projects",
                    "hidden": true
                },
                "mibig": {
                    "type": "boolean",
                    "description": "Set to true to download and include all MIBiG BGCs as input"
                },
                "genbank_input_buffer": {
                    "type": "integer",
                    "default": 50,
                    "description": "How many genbank files will be processed in a single task",
                    "help_text": "Decides how many parallel processes  will be used for genbank parsing; number of spawned parse processes = (# of input genomes) / (genbank_input_buffer)"
                },
                "defline_magic": {
                    "type": "boolean",
                    "help_text": "set to true if input fasta files contain uniprot deflines (sp| or tr|) (e.g. from uniprot fasta downloads) named defline_magic because may expand to other defline formats in the future",
                    "description": "set to true if input fasta files contain uniprot deflines (sp| or tr|)",
                    "hidden": true
                }
            }
        },
        "output_directories": {
            "title": "Output Directories",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "properties": {
                "outdir": {
                    "type": "string",
                    "description": "If set, and others not, all other outdirs within this directory",
                    "fa_icon": "fas fa-folder-open",
                    "default": "socialgene_results"
                },
                "outdir_download_cache": {
                    "type": "string",
                    "description": "Long term caching directory for use between different pipeline runs.",
                    "fa_icon": "fas fa-folder-open",
                    "default": "${params.outdir}/socialgene_long_cache",
                    "hidden": true
                },
                "outdir_per_run": {
                    "type": "string",
                    "description": "Directory that holds data generated each run",
                    "fa_icon": "fas fa-folder-open",
                    "default": "${params.outdir}/socialgene_per_run",
                    "hidden": true
                },
                "outdir_neo4j": {
                    "type": "string",
                    "description": "Path to the output directory where the results will be saved.",
                    "default": "${params.outdir}/socialgene_neo4j",
                    "fa_icon": "fas fa-folder-open",
                    "hidden": true
                },
                "outdir_genomes": {
                    "type": "string",
                    "default": "${params.outdir_per_run}",
                    "description": "Storage directory for downloaded genomes",
                    "fa_icon": "fas fa-folder-open",
                    "hidden": true
                },
                "outdir_blast_cache": {
                    "type": "string",
                    "default": "${params.outdir}/socialgene_per_run/blastp_cache",
                    "fa_icon": "fas fa-folder-open",
                    "description": "Cache folder where blast results are written to. Important to delete if starting a new pipeline run with different input data but using same cache directory as a previous run.",
                    "hidden": true
                },
                "tracedir": {
                    "type": "string",
                    "description": "Directory to keep pipeline Nextflow logs and reports.",
                    "default": "${params.outdir}/pipeline_info",
                    "fa_icon": "fas fa-folder-open",
                    "hidden": true
                }
            },
            "required": ["outdir"]
        },
        "socialgene_parameters": {
            "title": "SocialGene Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "fasta_splits": {
                    "type": "integer",
                    "default": 1,
                    "description": "Split non-redundant protein sequences into n-FASTA files",
                    "help_text": "Use this to run HMMER in parallel/make things faster. Determines how many FASTA files should be the created from all non-redundant protein sequences"
                },
                "hmm_splits": {
                    "type": "integer",
                    "default": 1,
                    "description": "For most use cases keep this at 1 and increase fasta_splits instead",
                    "help_text": "Determines how many hmm files should be created to run in parallel. This is mainly for making smaller files for massively parallel distribution on CHTC"
                },
                "include_sequences": {
                    "type": "boolean",
                    "description": "Include protein sequences in the Neo4j database?",
                    "default": true
                },
                "antismash_fulljson": {
                    "type": "boolean",
                    "description": "Keep full antismash output json? Can take up a lot of space for large datasets",
                    "hidden": true,
                    "default": true
                }
            }
        },
        "socialgene_modules": {
            "title": "SocialGene modules",
            "type": "object",
            "description": "These determine the annotations and structure of the resulting database",
            "default": "",
            "properties": {
                "build_database": {
                    "type": "boolean",
                    "default": true,
                    "description": "Should the Neo4j databse be created?"
                },
                "blastp": {
                    "type": "boolean",
                    "description": "Should all vs all  BLASTp be run? DO NOT RUN ON LARGE INPUT DATA WITHOUT STRICT FILTERS"
                },
                "hmmlist": {
                    "type": "string",
                    "description": "Comma-separated string (e.g. 'antismash,amrfinder) or 'all', see extended help for all options",
                    "help_text": "antismash,amrfinder,bigslice,classiphage, ipresto,pfam,prism,resfams,tigrfam,virus_orthologous_groups",
                    "hidden": true
                },
                "mmseqs_steps": {
                    "type": "string",
                    "description": "Descending, comma-delimited string of levels to cluster to- e.g. '90,80,70''"
                },
                "ncbi_taxonomy": {
                    "type": "boolean",
                    "description": "Download and insert the NCBI taxonomy database? Requires input assemblies to have NCBI  Assembly accessions"
                },
                "antismash": {
                    "type": "boolean",
                    "description": "Run antismash on all input genomes"
                },
                "chembl": {
                    "type": "boolean",
                    "description": "Include chembl data into database Not yet implemented",
                    "hidden": true
                },
                "paired_omics": {
                    "type": "boolean",
                    "description": "Not yet implemented",
                    "hidden": true
                },
                "goterms": {
                    "type": "boolean",
                    "description": "Download and process go term ontology"
                }
            }
        },
        "max_job_resources": {
            "title": "Max Job Resources",
            "type": "object",
            "fa_icon": "fab fa-acquisitions-incorporated",
            "description": "Set the top limit for requested resources for any single job.",
            "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that these values only set the max, to increase the actual resources requested by any single process you will need to set up your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
            "properties": {
                "max_cpus": {
                    "type": "integer",
                    "description": "Maximum number of CPUs that can be requested for any single job.",
                    "default": 8,
                    "fa_icon": "fas fa-microchip",
                    "help_text": "Used to set an upper-limit for the number of CPUs that can be used at once. Should be an integer e.g. `--max_cpus 1`\n\nhttps://www.nextflow.io/docs/latest/process.html#process-cpus"
                },
                "max_memory": {
                    "type": "string",
                    "description": "Maximum amount of memory that can be requested for any single job.",
                    "default": "24.GB",
                    "fa_icon": "fas fa-memory",
                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
                    "help_text": "Used to set an upper-limit for the memory any single process can use.  Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`\n\nhttps://www.nextflow.io/docs/latest/process.html#process-memory"
                },
                "max_time": {
                    "type": "string",
                    "description": "Maximum amount of time that can be requested for any single job.",
                    "default": "24.h",
                    "fa_icon": "far fa-clock",
                    "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
                    "help_text": "Used to set an upper-limit for the amount of time any single process is allowed to run. Should be a string in the format integer-unit e.g. `--max_time '2.h'`\n\nhttps://www.nextflow.io/docs/latest/process.html#time"
                },
                "slurm_queue_size": {
                    "type": "integer",
                    "default": 15,
                    "hidden": true,
                    "description": "Number of slurm jobs that can be running/submitted"
                }
            }
        },
        "advanced_hmm_input": {
            "title": "Advanced HMM Input",
            "type": "object",
            "description": "Any one or more of the following can be used to download/input HMMs for the pipeline",
            "default": "",
            "properties": {
                "custom_hmm_file": {
                    "type": "string",
                    "description": "File path of a custom HMMER hmm file",
                    "hidden": true
                },
                "domtblout_path": {
                    "type": "string",
                    "description": "Use externally-generated domtblout files. Please read the long description before using",
                    "help_text": "Use externally-generated domtblout files.\nThe models have to have the same name (identifier) as SocialGene expects, which is a SocialGene-generated hash of the HMM model",
                    "hidden": true
                },
                "domtblout_with_ga": {
                    "type": "string",
                    "description": "Path to hmmsearch results that used cutoffs",
                    "hidden": true
                },
                "domtblout_without_ga": {
                    "type": "string",
                    "description": "Path to hmmsearch results that didn't use cutoffs",
                    "hidden": true
                }
            }
        },
        "hmmer_options": {
            "title": "HMMER Options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "hmmsearch_model_threshold": {
                    "type": "string",
                    "default": "--cut_ga",
                    "description": "--cut_ga or --cut_nc or --cut_tc",
                    "help_text": "From HMMER documentation:\nOptions controlling model-specific thresholding:\n\n--cut_ga : use profile's GA gathering cutoffs to set all thresholding\n\n--cut_nc : use profile's NC noise cutoffs to set all thresholding\n\n--cut_tc : use profile's TC trusted cutoffs to set all thresholding\n",
                    "hidden": true
                },
                "HMMSEARCH_Z": {
                    "type": "integer",
                    "default": 100000000,
                    "description": "see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf",
                    "hidden": true
                },
                "HMMSEARCH_IEVALUE": {
                    "type": "number",
                    "default": 0.1,
                    "description": "see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf",
                    "hidden": true
                },
                "HMMSEARCH_E": {
                    "type": "number",
                    "default": 100,
                    "description": "see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf",
                    "hidden": true
                },
                "HMMSEARCH_DOME": {
                    "type": "number",
                    "default": 10,
                    "description": "see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf",
                    "hidden": true
                },
                "HMMSEARCH_INCE": {
                    "type": "number",
                    "default": 0.001,
                    "description": "see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf",
                    "hidden": true
                },
                "HMMSEARCH_INCDOME": {
                    "type": "number",
                    "default": 0.001,
                    "description": "see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf",
                    "hidden": true
                },
                "HMMSEARCH_SEED": {
                    "type": "integer",
                    "default": 42,
                    "description": "see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf",
                    "hidden": true
                },
                "HMMSEARCH_F1": {
                    "type": "number",
                    "default": 0.02,
                    "description": "see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf",
                    "hidden": true
                },
                "HMMSEARCH_F2": {
                    "type": "number",
                    "default": 0.001,
                    "description": "see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf",
                    "hidden": true
                },
                "HMMSEARCH_F3": {
                    "type": "number",
                    "default": 1e-5,
                    "description": "see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf",
                    "hidden": true
                }
            }
        },
        "external_data_versions": {
            "title": "External Data Versions",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "amrfinder_version": {
                    "type": "string",
                    "default": "2024-05-02.2",
                    "hidden": true,
                    "description": "Version of amrfinder to download/use"
                },
                "bigslice_version": {
                    "type": "string",
                    "default": "v1.0.0/bigslice-models.2020-04-27",
                    "hidden": true,
                    "description": "Version of bigslice to download/use"
                },
                "vog_version": {
                    "type": "string",
                    "default": "vog211",
                    "hidden": true,
                    "description": "Version of vog to download/use"
                },
                "tigrfam_version": {
                    "type": "string",
                    "default": "15",
                    "hidden": true,
                    "description": "Version of tigrfam to download/use"
                },
                "pfam_version": {
                    "type": "string",
                    "default": "37.0",
                    "description": "PFAM version. Ffor version numbers see: http://ftp.ebi.ac.uk/pub/databases/Pfam/releases",
                    "hidden": true
                },
                "antismash_hmms_git_sha": {
                    "type": "string",
                    "default": "8fd065a63e99ee628b536cc19fa66d5942b784ea",
                    "description": "Controls which version of antismash the antismash HMMS are pulled from",
                    "hidden": true
                },
                "chembl_version": {
                    "type": "string",
                    "description": "Set (e.g. '31' for chembl version 31) to incorporate chembl into the database",
                    "hidden": true,
                    "default": "31"
                }
            }
        },
        "htcondor_specific_parameters": {
            "title": "HTCONDOR specific parameters",
            "type": "object",
            "description": "These parameters are specific to UW-Madison's CHTC high throuput computing cluster",
            "default": "",
            "properties": {
                "htcondor": {
                    "type": "boolean",
                    "hidden": true,
                    "description": "Use the --htcondor flag to create files for htcondor, then run again with the results from the external run",
                    "help_text": "When --htcondor is set the pipeline will only run the steps required to generate and split the non-redundant FASTA file and HMM models for running on external hardware. (Don't delete the work directory until after the next step completes) This will result in a directory `$outdir/htcondor_cache` which contains all the data and scripts and instructions necessary to run highly-parallel `hmmsearch` on CHTC. Then the pipeline is run again, but replacing `--htcondor` with `--domtblout_path` and `--resume`, at which point the rest of the modules will also run.\n(Don't delete the work directory until all steps above complete)\n\nSee `https://github.com/socialgene/sgnf/blob/main/conf/examples/htcondor.config` for an example"
                },
                "htcondor_request_memory": {
                    "type": "string",
                    "default": "1GB",
                    "hidden": true,
                    "description": "See: https://chtc.cs.wisc.edu/uw-research-computing/helloworld"
                },
                "htcondor_request_cpus": {
                    "type": "integer",
                    "default": 1,
                    "hidden": true,
                    "description": "See: https://chtc.cs.wisc.edu/uw-research-computing/helloworld"
                },
                "htcondor_request_disk": {
                    "type": "string",
                    "default": "5GB",
                    "hidden": true,
                    "description": "See: https://chtc.cs.wisc.edu/uw-research-computing/helloworld"
                },
                "htcondor_max_idle": {
                    "type": "integer",
                    "default": 100,
                    "hidden": true,
                    "description": "See: https://chtc.cs.wisc.edu/uw-research-computing/helloworld"
                },
                "htcondor_squid_username": {
                    "type": "string",
                    "default": "cmclark8",
                    "hidden": true,
                    "description": "See: https://chtc.cs.wisc.edu/uw-research-computing/file-avail-squid"
                },
                "htcondor_WantGlideIn": {
                    "type": "boolean",
                    "default": true,
                    "hidden": true,
                    "description": "See: https://chtc.cs.wisc.edu/uw-research-computing/helloworld"
                },
                "htcondor_WantFlocking": {
                    "type": "boolean",
                    "default": true,
                    "hidden": true,
                    "description": "See: https://chtc.cs.wisc.edu/uw-research-computing/helloworld"
                },
                "htcondor_prep_directory": {
                    "type": "string",
                    "default": "socialgene_results/htcondor_cache",
                    "hidden": true,
                    "description": "Where data to be sent to CHTC will be written"
                }
            }
        },
        "multiqc": {
            "title": "MULTIQC",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "multiqc_title": {
                    "type": "string",
                    "description": "x",
                    "hidden": true
                },
                "multiqc_logo": {
                    "type": "string",
                    "description": "x",
                    "hidden": true
                },
                "multiqc_config": {
                    "type": "string",
                    "description": "x",
                    "hidden": true
                },
                "max_multiqc_email_size": {
                    "type": "string",
                    "default": "25.MB",
                    "description": "x",
                    "hidden": true
                },
                "multiqc_methods_description": {
                    "type": "string",
                    "description": "x",
                    "hidden": true
                }
            }
        },
        "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": {
                "help": {
                    "type": "boolean",
                    "description": "Display help text.",
                    "fa_icon": "fas fa-question-circle",
                    "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
                },
                "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
                },
                "validationShowHiddenParams": {
                    "type": "boolean",
                    "fa_icon": "far fa-eye-slash",
                    "description": "Show all params when using `--help`",
                    "hidden": true,
                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
                },
                "hook_url": {
                    "type": "string",
                    "hidden": true,
                    "description": "x"
                },
                "version": {
                    "type": "boolean",
                    "description": "Display version and exit.",
                    "fa_icon": "fas fa-question-circle",
                    "hidden": true
                },
                "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})$",
                    "hidden": true
                },
                "input": {
                    "type": "string",
                    "description": "not used, required by nf-core linter",
                    "hidden": true
                },
                "sort_fasta": {
                    "type": "boolean",
                    "description": "BLAST (and maybe MMseqs2?) differ based on sequence order, setting this to true will sort the protein fasta file first (note: this will make a copy of the data)",
                    "hidden": true
                },
                "publish_dir_mode": {
                    "type": "string",
                    "default": "copy",
                    "description": "mode for publishing results form work directories"
                }
            }
        },
        "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"
                }
            }
        },
        "docker_images": {
            "title": "Docker Images",
            "type": "object",
            "description": "Change the docker image tags (advanced, for developers)",
            "default": "",
            "properties": {
                "sgnf_antismash_dockerimage": {
                    "type": "string",
                    "hidden": true,
                    "description": "Specify which docker image tag to use (default is the version synced to pipeline version number)"
                },
                "sgnf_hmmer_dockerimage": {
                    "type": "string",
                    "hidden": true,
                    "description": "Specify which docker image tag to use (default is the version synced to pipeline version number)"
                },
                "sgnf_hmmer_plus_dockerimage": {
                    "type": "string",
                    "hidden": true,
                    "description": "Specify which docker image tag to use (default is the version synced to pipeline version number)"
                },
                "sgnf_sgpy_dockerimage": {
                    "type": "string",
                    "hidden": true,
                    "description": "Specify which docker image tag to use (default is the version synced to pipeline version number)"
                },
                "sgnf_minimal_dockerimage": {
                    "type": "string",
                    "hidden": true,
                    "description": "Specify which docker image tag to use (default is the version synced to pipeline version number)"
                }
            }
        },
        "validation": {
            "title": "Validation",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "validationFailUnrecognisedParams": {
                    "type": "boolean",
                    "hidden": true
                },
                "validationLenientMode": {
                    "type": "boolean",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/input_genomes"
        },
        {
            "$ref": "#/definitions/output_directories"
        },
        {
            "$ref": "#/definitions/socialgene_parameters"
        },
        {
            "$ref": "#/definitions/socialgene_modules"
        },
        {
            "$ref": "#/definitions/max_job_resources"
        },
        {
            "$ref": "#/definitions/advanced_hmm_input"
        },
        {
            "$ref": "#/definitions/hmmer_options"
        },
        {
            "$ref": "#/definitions/external_data_versions"
        },
        {
            "$ref": "#/definitions/htcondor_specific_parameters"
        },
        {
            "$ref": "#/definitions/multiqc"
        },
        {
            "$ref": "#/definitions/generic_options"
        },
        {
            "$ref": "#/definitions/institutional_config_options"
        },
        {
            "$ref": "#/definitions/docker_images"
        },
        {
            "$ref": "#/definitions/validation"
        }
    ],
    "properties": {
        "prism_hmms_git_sha": {
            "type": "string",
            "default": "4bf8bbdf2da3b4f1c764de2301be7b02e74af157"
        },
        "fasta_csv": {
            "type": "string"
        },
        "genbank_csv": {
            "type": "string"
        },
        "fna_csv": {
            "type": "string"
        }
    }
}