nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/sanger-tol/readmapping/main/nextflow_schema.json",
    "title": "sanger-tol/readmapping pipeline parameters",
    "description": "Pipeline to map reads generated using different sequencing technologies against a genome assembly.",
    "type": "object",
    "$defs": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": ["input", "outdir", "outfmt", "compression"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_input.json",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "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 at least 4 columns, and a header row.",
                    "fa_icon": "fas fa-file-csv"
                },
                "outdir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                    "fa_icon": "fas fa-folder-open"
                },
                "outfmt": {
                    "type": "string",
                    "default": "cram",
                    "description": "Format for output alignment files. Accepts options: \"bam\" or \"cram\".",
                    "fa_icon": "fas fa-file-signature"
                },
                "compression": {
                    "type": "string",
                    "default": "crumble",
                    "description": "Output file compression type. Currently accepts: \"none\" or \"crumble\"",
                    "fa_icon": "fas fa-file-archive"
                },
                "merge_output": {
                    "type": "string",
                    "description": "Set to a non-empty string to merge output alignment files by specimens. The string is used to name the output directory",
                    "fa_icon": "fas fa-layer-group"
                },
                "window_size": {
                    "type": "integer",
                    "default": 1000,
                    "description": "Bin size (in bp) used for computing coverage depth in the output bedGraph file.",
                    "fa_icon": "fas fa-chart-bar",
                    "minimum": 1
                },
                "pacbio_adapter_fasta": {
                    "type": "string",
                    "description": "Path to FASTA file contains adapter sequences for PacBio HiFi reads.",
                    "format": "file-path",
                    "default": "${projectDir}/assets/HiFi_adapter.fasta",
                    "fa_icon": "fas fa-bezier-curve"
                },
                "pacbio_adapter_yaml": {
                    "type": "string",
                    "description": "Path to YAML file containing guide for trimming/filtering PacBio data. See hifi-trimmer docs for details: https://github.com/sanger-tol/hifi-trimmer",
                    "help_text": "YAML file containing adapter sequences and trimming parameters for PacBio HiFi data processing. This file guides hifi-trimmer in identifying and removing adapter contamination from HiFi reads. For more information about the expected format and configuration options, see the hifi-trimmer documentation: https://github.com/sanger-tol/hifi-trimmer",
                    "format": "file-path",
                    "default": "${projectDir}/assets/HiFi_adapter.yaml",
                    "fa_icon": "far fa-file-code"
                },
                "pacbio_uli_adapter": {
                    "type": "string",
                    "description": "Path to FASTA file containing the PacBio ULI adapter sequence.",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                    "fa_icon": "far fa-file-code"
                },
                "email": {
                    "type": "string",
                    "description": "Email address for completion summary.",
                    "fa_icon": "fas fa-envelope",
                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
                }
            }
        },
        "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.",
            "required": ["fasta"],
            "properties": {
                "fasta": {
                    "type": "string",
                    "description": "Path to FASTA genome file.",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                    "fa_icon": "far fa-file-code"
                },
                "header": {
                    "type": "string",
                    "format": "file-path",
                    "description": "Optional template header file for BAM/CRAM outputs",
                    "fa_icon": "far fa-file-code"
                }
            }
        },
        "aligner_options": {
            "title": "Aligner options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "short_aligner": {
                    "type": "string",
                    "default": "bwamem2",
                    "description": "Alignment method to use for short-reads (options are: \"minimap2\" or \"bwamem2\"",
                    "enum": ["minimap2", "bwamem2"]
                },
                "long_reads_map_chunk_size": {
                    "type": "integer",
                    "default": 10000,
                    "description": "Chunk size for parallel alignment of long read data, in number of sequences",
                    "minimum": 1
                },
                "short_reads_map_chunk_size": {
                    "type": "integer",
                    "default": 10000,
                    "description": "Chunk size for parallel alignment of short read data, in number of cram containers",
                    "minimum": 1
                }
            }
        },
        "execution": {
            "title": "Execution",
            "type": "object",
            "description": "Control the execution of the pipeline.",
            "default": "",
            "properties": {
                "use_work_dir_as_temp": {
                    "type": "boolean",
                    "description": "Set to true to make tools (e.g. sort, FastK, MerquryFK) use the work directory for their temporary files, rather than the system default.",
                    "fa_icon": "fas fa-arrow-circle-down",
                    "hidden": true
                }
            },
            "fa_icon": "fas fa-running"
        },
        "institutional_config_options": {
            "title": "Institutional config options",
            "type": "object",
            "fa_icon": "fas fa-university",
            "description": "Parameters used to describe centralised config profiles. These should not be edited.",
            "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
            "properties": {
                "custom_config_version": {
                    "type": "string",
                    "description": "Git commit id for Institutional configs.",
                    "default": "master",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "custom_config_base": {
                    "type": "string",
                    "description": "Base directory for Institutional configs.",
                    "default": "https://raw.githubusercontent.com/nf-core/configs/master",
                    "hidden": true,
                    "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_name": {
                    "type": "string",
                    "description": "Institutional config name.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_description": {
                    "type": "string",
                    "description": "Institutional config description.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_contact": {
                    "type": "string",
                    "description": "Institutional config contact information.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_url": {
                    "type": "string",
                    "description": "Institutional config URL link.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                }
            }
        },
        "generic_options": {
            "title": "Generic options",
            "type": "object",
            "fa_icon": "fas fa-file-import",
            "description": "Less common options for the pipeline, typically set in a config file.",
            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
            "properties": {
                "version": {
                    "type": "boolean",
                    "description": "Display version and exit.",
                    "fa_icon": "fas fa-question-circle",
                    "hidden": true
                },
                "publish_dir_mode": {
                    "type": "string",
                    "default": "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
                },
                "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_title": {
                    "type": "string",
                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                    "fa_icon": "fas fa-file-signature"
                },
                "multiqc_config": {
                    "type": "string",
                    "format": "file-path",
                    "description": "Custom config file to supply to MultiQC.",
                    "fa_icon": "fas fa-cog",
                    "hidden": true
                },
                "multiqc_logo": {
                    "type": "string",
                    "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
                    "fa_icon": "fas fa-image",
                    "format": "path"
                },
                "multiqc_methods_description": {
                    "type": "string",
                    "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                    "fa_icon": "fas fa-cog"
                },
                "validate_params": {
                    "type": "boolean",
                    "description": "Boolean whether to validate parameters against the schema at runtime",
                    "default": true,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "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)."
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/$defs/input_output_options"
        },
        {
            "$ref": "#/$defs/reference_genome_options"
        },
        {
            "$ref": "#/$defs/aligner_options"
        },
        {
            "$ref": "#/$defs/execution"
        },
        {
            "$ref": "#/$defs/institutional_config_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        }
    ]
}