{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/isoseq/master/nextflow_schema.json",
    "title": "nf-core/isoseq pipeline parameters",
    "description": "Genes and transcripts annotation with Isoseq using uLTRA and TAMA",
    "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": ["input", "outdir", "primers"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/csv",
                    "schema": "assets/schema_input.json",
                    "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/isoseq/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "primers": {
                    "type": "string",
                    "fa_icon": "fas fa-grip-lines",
                    "description": "Fasta file of primers sequences",
                    "help_text": "The provided file must contains all primers sequences used for sequencing. \nGziped files are accepted. "
                },
                "gtf": {
                    "type": "string",
                    "fa_icon": "fas fa-stream",
                    "description": "Genome annotation file",
                    "help_text": "Provide a GTF annotation file (sorted by sequence and start) if you set the `--aligner` option to `uLTRA`\nGziped files are accepted. "
                },
                "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",
                    "default": "results"
                },
                "email": {
                    "type": "string",
                    "description": "Email address for completion summary.",
                    "fa_icon": "fas fa-envelope",
                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
                },
                "multiqc_title": {
                    "type": "string",
                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                    "fa_icon": "fas fa-file-signature"
                }
            }
        },
        "ccs_options": {
            "title": "CCS options",
            "type": "object",
            "description": "Use these options to set CCS parameters",
            "default": "",
            "properties": {
                "chunk": {
                    "type": "integer",
                    "default": 40,
                    "description": "ccs --chunk option, define the number of batches to run in parallel",
                    "help_text": "CCS workload can be split into to chunks for a faster running time. \nThis value must be a positive integer greater than 1. \n```bash\n--chunk 1/10 \n```",
                    "fa_icon": "fas fa-cog"
                },
                "rq": {
                    "type": "number",
                    "default": 0.9,
                    "description": "ccs --rq option, define the minimum read quality for CCS selection",
                    "help_text": "Minimum read quality for a consensus. \nUnder this threshold the sequence is discarded. \nThis value must be in range [0-1]. \n```bash\n--rq 0.9\n```",
                    "fa_icon": "fas fa-cog"
                },
                "min_passes": {
                    "type": "integer",
                    "default": 3,
                    "description": "ccs --min-passes option, define the minimum number of passes to select a CCS",
                    "help_text": "Minimum number of full-length subreads required to generate CCS for a ZMW.",
                    "fa_icon": "fas fa-cog"
                },
                "min_snr": {
                    "type": "number",
                    "default": 2.5,
                    "description": "ccs --min-snr option, minimum SNR of subreads to use for generating CCS",
                    "help_text": "Minimum SNR of subreads to use for generating CCS",
                    "fa_icon": "fas fa-cog"
                },
                "min_length": {
                    "type": "integer",
                    "default": 10,
                    "description": "ccs --min-length option, minimum CCS length for CCS selection",
                    "help_text": "Minimum draft length before polishing",
                    "fa_icon": "fas fa-cog"
                },
                "max_length": {
                    "type": "integer",
                    "default": 50000,
                    "description": "ccs --max-length option, maximum CCS length for CCS selection",
                    "help_text": "Maximum draft length before polishing",
                    "fa_icon": "fas fa-cog"
                },
                "top_passes": {
                    "type": "integer",
                    "default": 60,
                    "description": "ccs --top-passes option, maximum number of passes to use for CCS generation",
                    "help_text": "Pick at maximum the top N passes for each ZMW",
                    "fa_icon": "fas fa-cog"
                }
            },
            "fa_icon": "fas fa-cogs"
        },
        "aligner_option": {
            "title": "Aligner option",
            "type": "object",
            "description": "Aligner selection",
            "default": "",
            "fa_icon": "fas fa-stream",
            "properties": {
                "aligner": {
                    "type": "string",
                    "description": "Aligner to use for mapping: minimap2 or ultra",
                    "help_text": "The `uLTRA` aligner improve detection of small exons but require an annotation in GTF format to run. \nIf the genome don't have any reference annotation, you have to use `minimap2`. ",
                    "fa_icon": "fas fa-stream",
                    "enum": ["minimap2", "ultra"]
                }
            },
            "required": ["aligner"]
        },
        "tama_options": {
            "title": "TAMA options",
            "type": "object",
            "description": "Use these options to set TAMA collapse and TAMA merge parameters",
            "default": "",
            "properties": {
                "capped": {
                    "type": "boolean",
                    "description": "TAMA collapse: Capped RNA?",
                    "help_text": "Set this option if the RNAs are capped. \n```bash\n--capped\n```",
                    "fa_icon": "fas fa-graduation-cap"
                },
                "five_prime": {
                    "type": "integer",
                    "default": 100,
                    "description": "TAMA collapse: 5 prime wobble threshold",
                    "help_text": "Set the maximum threshold for collapsing 5 prime exon.\n```\n--five_prime 100\n```",
                    "fa_icon": "fas fa-cog"
                },
                "splice_junction": {
                    "type": "integer",
                    "default": 10,
                    "description": "TAMA collapse: Splice junction / exon wobble threshold",
                    "help_text": "Set the maximum threshold for collapsing spliced exons.\n```\n--splice_junction 10\n```",
                    "fa_icon": "fas fa-cog"
                },
                "three_prime": {
                    "type": "integer",
                    "default": 100,
                    "description": "TAMA collapse: 3 prime wobble threshold",
                    "help_text": "Set the maximum threshold for collapsing 3 prime exon.\n```\n--three_prime 100\n```",
                    "fa_icon": "fas fa-cog"
                }
            },
            "fa_icon": "fas fa-cogs"
        },
        "reference_genome_options": {
            "title": "Reference genome options",
            "type": "object",
            "fa_icon": "fas fa-dna",
            "description": "Reference genome related files and options required for the workflow.",
            "properties": {
                "genome": {
                    "type": "string",
                    "description": "Name of iGenomes reference.",
                    "fa_icon": "fas fa-book",
                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
                },
                "fasta": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                    "description": "Path to FASTA genome file.",
                    "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs. Gziped files are accepted. ",
                    "fa_icon": "far fa-file-code"
                },
                "igenomes_base": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Directory / URL base for iGenomes references.",
                    "default": "s3://ngi-igenomes/igenomes",
                    "fa_icon": "fas fa-cloud-download-alt",
                    "hidden": true
                },
                "igenomes_ignore": {
                    "type": "boolean",
                    "description": "Do not load the iGenomes reference config.",
                    "fa_icon": "fas fa-ban",
                    "hidden": true,
                    "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
                }
            }
        },
        "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"
                }
            }
        },
        "max_job_request_options": {
            "title": "Max job request options",
            "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 you can not _increase_ the resources requested by any job using these options. For that you will need 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": 16,
                    "fa_icon": "fas fa-microchip",
                    "hidden": true,
                    "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
                },
                "max_memory": {
                    "type": "string",
                    "description": "Maximum amount of memory that can be requested for any single job.",
                    "default": "128.GB",
                    "fa_icon": "fas fa-memory",
                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
                    "hidden": true,
                    "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
                },
                "max_time": {
                    "type": "string",
                    "description": "Maximum amount of time that can be requested for any single job.",
                    "default": "240.h",
                    "fa_icon": "far fa-clock",
                    "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
                    "hidden": true,
                    "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
                }
            }
        },
        "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
                },
                "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
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "hidden": true
                },
                "hook_url": {
                    "type": "string",
                    "description": "Incoming hook URL for messaging service",
                    "fa_icon": "fas fa-people-group",
                    "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                    "hidden": true
                },
                "multiqc_config": {
                    "type": "string",
                    "description": "Custom config file to supply to MultiQC.",
                    "fa_icon": "fas fa-cog",
                    "hidden": true
                },
                "multiqc_logo": {
                    "type": "string",
                    "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
                    "fa_icon": "fas fa-image",
                    "hidden": true
                },
                "multiqc_methods_description": {
                    "type": "string",
                    "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                    "fa_icon": "fas fa-cog"
                },
                "tracedir": {
                    "type": "string",
                    "description": "Directory to keep pipeline Nextflow logs and reports.",
                    "default": "${params.outdir}/pipeline_info",
                    "fa_icon": "fas fa-cogs",
                    "hidden": true
                },
                "validate_params": {
                    "type": "boolean",
                    "description": "Boolean whether to validate parameters against the schema at runtime",
                    "default": true,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "show_hidden_params": {
                    "type": "boolean",
                    "fa_icon": "far fa-eye-slash",
                    "description": "Show all params when using `--help`",
                    "hidden": true,
                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/ccs_options"
        },
        {
            "$ref": "#/definitions/aligner_option"
        },
        {
            "$ref": "#/definitions/tama_options"
        },
        {
            "$ref": "#/definitions/reference_genome_options"
        },
        {
            "$ref": "#/definitions/institutional_config_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ]
}
