nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/pfizer-opensource/nf-crispr-pooled-screen/master/nextflow_schema.json",
    "title": "pfizer-opensource/nf-crispr-pooled-screen pipeline parameters",
    "description": "CRISPR pooled screening analysis",
    "type": "object",
    "definitions": {
        "input_output_options": {
            "title": "Input and output",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "properties": {
                "fastq_dir": {
                    "type": "string",
                    "format": "directory-path",
                    "title": "FASTQ directory",
                    "description": "The input directory containing fastq files. Use absolute paths for storage on cloud infrastructure.",
                    "fa_icon": "fas fa-folder-open"
                },
                "metadata": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.csv",
                    "title": "Upload metadata file",
                    "description": "Path to metadata input file.",
                    "fa_icon": "far fa-file-code"
                },
                "metadata_format": {
                    "type": "string",
                    "default": "illumina",
                    "enum": ["illumina", "csv"],
                    "title": "Selet metadata format",
                    "description": "The format of the metadata file.",
                    "fa_icon": "far fa-file-code"
                },
                "library": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.txt",
                    "title": "Upload guide library file",
                    "description": "Path to the guide library file.",
                    "fa_icon": "far fa-file-code"
                },
                "prefix": {
                    "type": "string",
                    "title": "Experiment prefix",
                    "description": "Prefix added to the output file names.",
                    "fa_icon": "far fa-file-code"
                },
                "outdir": {
                    "type": "string",
                    "default": "output",
                    "format": "directory-path",
                    "title": "Output directory",
                    "description": "The output directory where the results will be saved.",
                    "fa_icon": "fas fa-folder-open",
                    "portal_hidden": true
                }
            },
            "required": ["fastq_dir", "metadata", "library", "prefix"]
        },
        "preprocess_qc_options": {
            "title": "Preprocessing and QC",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Options controlling preprocessing (including guide counting) and quality control analysis",
            "properties": {
                "count_program": {
                    "type": "string",
                    "default": "mageck",
                    "enum": ["mageck"],
                    "title": "Select guide count program",
                    "description": "Program to use to count guide reads.",
                    "fa_icon": "fas fa-question-circle"
                },
                "normalization_method": {
                    "type": "string",
                    "default": "median",
                    "title": "Select guide normalization method",
                    "description": "Method to use for guide count normalization.",
                    "fa_icon": "far fa-file-code",
                    "enum": ["none", "median", "total", "control"]
                },
                "control_guides": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.txt",
                    "title": "Upload control guides file",
                    "description": "Path to file containing control guides for control normalization.",
                    "fa_icon": "far fa-file-code"
                },
                "mageck_count_options": {
                    "type": "string",
                    "pattern": "^\\s*(--?\\S+(\\s+[^-]\\S+)?\\s*)+$",
                    "title": "MAGeCK count additional options",
                    "description": "Additional options for the mageck count command.",
                    "fa_icon": "far fa-file-code"
                },
                "annotate_dictionary": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.yml",
                    "title": "Upload gene annotation file",
                    "description": "Path to YAML file defining the gene annotation dictionary.",
                    "fa_icon": "far fa-file-code",
                    "hidden": true
                }
            }
        },
        "analysis_options": {
            "title": "Analysis",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Screen analysis options",
            "properties": {
                "run_mageck_mle": {
                    "type": "boolean",
                    "title": "Perform MAGeCK MLE analysis?",
                    "description": "Whether to run the MAGeCK MLE analysis.",
                    "fa_icon": "fas fa-gears"
                },
                "design_matrix": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.txt",
                    "title": "Upload design matrix file",
                    "description": "Path to the mageck mle design matrix.",
                    "fa_icon": "far fa-file-code"
                },
                "mageck_mle_options": {
                    "type": "string",
                    "pattern": "^\\s*(--?\\S+(\\s+[^-]\\S+)?\\s*)+$",
                    "title": "MAGeCK MLE additional options",
                    "description": "Additional options for the mageck mle command.",
                    "fa_icon": "far fa-file-code"
                },
                "run_mageck_test": {
                    "type": "boolean",
                    "title": "Perform MAGeCK test analysis?",
                    "description": "Whether to run the MAGeCK test analysis.",
                    "fa_icon": "fas fa-gears"
                },
                "gene_test_threshold": {
                    "type": "number",
                    "default": 0.25,
                    "minimum": 0,
                    "maximum": 1,
                    "title": "Gene test threshold",
                    "description": "Threshold for including guides in the gene test in MAGeCK test",
                    "fa_icon": "fas fa-sliders"
                },
                "gene_lfc_method": {
                    "type": "string",
                    "default": "alphamedian",
                    "enum": ["median", "alphamedian", "mean", "alphamean", "secondbest"],
                    "title": "Select gene LFC method",
                    "description": "Method for calculating gene log fold change from guide LFCs in MAGeCK test",
                    "fa_icon": "fas fa-sliders"
                },
                "mageck_test_options": {
                    "type": "string",
                    "pattern": "^\\s*(--?\\S+(\\s+[^-]\\S+)?\\s*)+$",
                    "title": "MAGeCK test additional options",
                    "description": "Additional options for the mageck test command.",
                    "fa_icon": "far fa-file-code"
                }
            }
        },
        "max_job_request_options": {
            "title": "Max job request options",
            "type": "object",
            "fa_icon": "fab fa-acquisitions-incorporated",
            "description": "Set the top limit for requested resources for any single job.",
            "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
            "properties": {
                "max_cpus": {
                    "type": "integer",
                    "description": "Maximum number of CPUs that can be requested for any single job.",
                    "default": 16,
                    "fa_icon": "fas fa-microchip",
                    "hidden": true,
                    "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
                },
                "max_memory": {
                    "type": "string",
                    "description": "Maximum amount of memory that can be requested for any single job.",
                    "default": "10.GB",
                    "fa_icon": "fas fa-memory",
                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
                    "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": "4.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": {
                    "type": "string",
                    "description": "Email address for completion summary, only when pipeline fails.",
                    "fa_icon": "fas fa-envelope",
                    "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",
                    "hidden": true
                },
                "plaintext_email": {
                    "type": "boolean",
                    "description": "Send plain-text email instead of HTML.",
                    "fa_icon": "fas fa-remove-format",
                    "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
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "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/preprocess_qc_options"
        },
        {
            "$ref": "#/definitions/analysis_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ]
}