nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/tfactivity/master/nextflow_schema.json",
    "title": "nf-core/tfactivity pipeline parameters",
    "description": "TBD",
    "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"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_input.json",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/tfactivity/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "input_bam": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_input_bam.json",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "description": "Path to comma-separated file containing information about the BAM files in the experiment.",
                    "help_text": "You will need to create a design file with information about the BAM files in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row. See [usage docs](https://nf-co.re/tfactivity/usage#bam-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "counts": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.(csv|txt)$",
                    "description": "Path to comma-separated file containing the counts for the samples in the experiment. Can also be a file containing just gene identifiers. In this case, count values need to be referenced in the counts_design file.",
                    "help_text": "You will need to create a counts file with the counts for the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/tfactivity/usage#counts-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "counts_design": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_counts_design.json",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "description": "Path to comma-separated file containing information about the counts file.",
                    "help_text": "You will need to create a counts design file with information about the counts file 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/tfactivity/usage#counts-design-input).",
                    "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"
                },
                "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"
                }
            }
        },
        "pipeline_options": {
            "title": "Pipeline options",
            "type": "object",
            "fa_icon": "fas fa-cogs",
            "description": "Options for the pipeline itself.",
            "properties": {
                "merge_samples": {
                    "type": "boolean",
                    "description": "Merge samples with the same condition and assay.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "If you have multiple samples with the same condition and assay, you can set this parameter to `true` to merge them into a single sample. This is useful if you have technical replicates and want to combine them into a single sample for analysis."
                },
                "min_peak_occurrence": {
                    "type": "integer",
                    "default": 1,
                    "description": "Minimum number of samples that a peak has to occur in to keep it while merging.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "If you have multiple samples with the same condition and assay and use the `--merge_samples` parameter, you can set this parameter to the minimum number of samples that a peak has to occur in to keep it while merging."
                },
                "window_size": {
                    "type": "integer",
                    "default": 50000,
                    "description": "Size of the window to search for binding sites.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Size of the window to search for binding sites. The default value is 50000."
                },
                "decay": {
                    "type": "boolean",
                    "default": "true",
                    "description": "Use decay in STARE",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Use decay in STARE. The default value is `true`."
                },
                "expression_aggregation": {
                    "type": "string",
                    "default": "mean",
                    "description": "Method to aggregate expression values.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Method to aggregate expression values. The default value is `mean`."
                },
                "affinity_aggregation": {
                    "type": "string",
                    "default": "max",
                    "description": "Method to aggregate affinity values.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Method to aggregate affinity values. The default value is `max`."
                },
                "chromhmm_states": {
                    "type": "integer",
                    "default": 10,
                    "description": "Number of ChromHMM states.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Number of ChromHMM states. The default value is 10."
                },
                "chromhmm_threshold": {
                    "type": "number",
                    "default": 0.75,
                    "description": "Threshold for ChromHMM enhancer detection.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Threshold for ChromHMM enhancer detection. The default value is 0.9."
                },
                "chromhmm_enhancer_marks": {
                    "type": "string",
                    "default": "H3K27ac,H3K4me1",
                    "description": "Comma-separated ChromHMM enhancer marks.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "ChromHMM enhancer marks. The default value is `H3K27ac`."
                },
                "chromhmm_promoter_marks": {
                    "type": "string",
                    "default": "H3K4me3",
                    "description": "Comma-separated ChromHMM promoter marks.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "ChromHMM promoter marks. The default value is `H3K4me3`."
                },
                "rose_tss_window": {
                    "type": "integer",
                    "default": 2500,
                    "description": "TSS window in base pairs",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "ROSE window size around transcription start sites"
                },
                "rose_stitching_window": {
                    "type": "integer",
                    "default": 12500,
                    "description": "Stichting window in base pairs",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "ROSE window size for stitching two regions together"
                },
                "min_count": {
                    "type": "integer",
                    "default": 50,
                    "description": "Minimum number of total counts to keep a gene in the analysis.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Minimum number of total counts to keep a gene in the analysis. The default value is 50."
                },
                "min_tpm": {
                    "type": "number",
                    "default": 1,
                    "description": "Minimum TPM to keep a gene in the analysis.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Minimum TPM to keep a gene in the analysis. The default value is 1."
                },
                "min_count_tf": {
                    "type": "integer",
                    "default": 50,
                    "description": "Minimum number of total counts to keep a transcription factor in the analysis.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Minimum number of total counts to keep a transcription factor in the analysis. The default value is 50."
                },
                "min_tpm_tf": {
                    "type": "number",
                    "default": 1,
                    "description": "Minimum TPM to keep a transcription factor in the analysis.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Minimum TPM to keep a transcription factor in the analysis. The default value is 1."
                },
                "dynamite_ofolds": {
                    "type": "integer",
                    "default": 3,
                    "description": "Number of outer folds for dynamite.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Number of outer folds for dynamite. The default value is 3."
                },
                "dynamite_ifolds": {
                    "type": "integer",
                    "default": 6,
                    "description": "Number of inner folds for dynamite.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Number of inner folds for dynamite. The default value is 6."
                },
                "dynamite_alpha": {
                    "type": "number",
                    "default": 0.1,
                    "description": "Alpha value for dynamite.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Alpha value for dynamite. The default value is 0.1."
                },
                "dynamite_randomize": {
                    "type": "boolean",
                    "default": "false",
                    "description": "Randomize the data for dynamite.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Randomize the data for dynamite. The default value is `false`."
                },
                "dynamite_min_regression": {
                    "type": "number",
                    "default": 0.1,
                    "description": "Minimum regression value for dynamite.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Minimum regression value for dynamite. The default value is 0.1."
                },
                "alpha": {
                    "type": "number",
                    "default": 0.05,
                    "description": "Alpha value for the Mann-Whitney U test.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Alpha value for the Mann-Whitney U test. The default value is 0.05."
                }
            }
        },
        "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",
                    "exists": true,
                    "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.",
                    "fa_icon": "far fa-file-code"
                },
                "gtf": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.gtf(\\.gz)?$",
                    "description": "Path to GTF gene annotation file.",
                    "help_text": "This parameter is *mandatory* if `--genome` is not specified.",
                    "fa_icon": "far fa-file-code"
                },
                "blacklist": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.bed(\\.gz)?$",
                    "description": "Path to blacklist regions file.",
                    "help_text": "This parameter is *mandatory* if `--genome` is not specified.",
                    "fa_icon": "far fa-file-code"
                },
                "motifs": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.(cisbp|homer|jaspar|meme|transfac|uniprobe)?$",
                    "description": "Path to transcription factor motifs file.",
                    "help_text": "This parameter is *mandatory* if `--genome` is not specified. Alternatively, you can use the `--taxon_id` parameter to fetch the motifs from the JASPAR database.",
                    "fa_icon": "far fa-file-code"
                },
                "taxon_id": {
                    "type": "integer",
                    "description": "NCBI Taxonomy ID.",
                    "fa_icon": "fas fa-dna",
                    "help_text": "This parameter is *mandatory* if `--genome` and `--motifs` are not specified. Use this parameter to fetch the motifs from the JASPAR database."
                },
                "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|d|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",
                    "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",
                    "hidden": true
                },
                "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
                },
                "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."
                },
                "validationFailUnrecognisedParams": {
                    "type": "boolean",
                    "fa_icon": "far fa-check-circle",
                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
                    "hidden": true,
                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
                },
                "validationLenientMode": {
                    "type": "boolean",
                    "fa_icon": "far fa-check-circle",
                    "description": "Validation of parameters in lenient more.",
                    "hidden": true,
                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
                },
                "pipelines_testdata_base_path": {
                    "type": "string",
                    "fa_icon": "far fa-check-circle",
                    "description": "Base URL or local path to location of pipeline test dataset files",
                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/pipeline_options"
        },
        {
            "$ref": "#/definitions/reference_genome_options"
        },
        {
            "$ref": "#/definitions/institutional_config_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ]
}