nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/pixelator/master/nextflow_schema.json",
    "title": "nf-core/pixelator pipeline parameters",
    "description": "Pipeline for analysis of Proximity Network Assay data",
    "type": "object",
    "$defs": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": ["input", "outdir"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_input.json",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.(csv|tsv|yml|yaml)$",
                    "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/pixelator/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "input_basedir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Path to a local or remote directory that is the \"current working directory\" for relative paths defined in the input samplesheet",
                    "fa_icon": "fas fa-folder"
                },
                "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})$"
                }
            }
        },
        "pna_amplicon_options": {
            "title": "Amplicon options",
            "type": "object",
            "fa_icon": "fas fa-dna",
            "properties": {
                "save_pna_amplicon_reads": {
                    "fa_icon": "fas fa-save",
                    "type": "boolean",
                    "description": "Save intermediate amplicon reads generated from the raw input reads.",
                    "help": "By default, generated amplicon FastQ files will not be saved to the results directory. Specify this flag (or set it to `true` in your config file) to copy these files to the results directory when complete."
                },
                "pna_amplicon_mismatches": {
                    "type": "number",
                    "fa_icon": "fas fa-not-equal",
                    "minimum": 0,
                    "maximum": 0.5,
                    "description": "The number of mismatches allowed while anchoring reads using LBS sequences (in percentage of seen LBS length) [default: 0.1; 0.0<=x<=0.5]",
                    "default": 0.1
                },
                "pna_amplicon_remove_polyg": {
                    "description": "Remove PolyG sequences (length of 10 or more)",
                    "fa_icon": "fas fa-cut",
                    "type": "boolean",
                    "default": true
                },
                "pna_amplicon_quality_cutoff": {
                    "description": "Minimum average quality a read must have. Pass 0 to disable quality filtering.",
                    "fa_icon": "fas fa-sliders-h",
                    "type": "integer",
                    "default": 20
                },
                "pna_amplicon_low_complexity_filter": {
                    "type": "boolean",
                    "fa_icon": "fas fa-filter",
                    "default": true,
                    "description": "Enable filtering of amplicons with low complexity UMI sequences."
                },
                "pna_amplicon_low_complexity_threshold": {
                    "type": "number",
                    "fa_icon": "fas fa-percentage",
                    "default": 0.8,
                    "minimum": 0.5,
                    "maximum": 1,
                    "description": "The threshold for determining if a UMI sequence is of low complexity and will be removed. [0.5<=x<=1.0]"
                },
                "pna_amplicon_lbs_filter": {
                    "type": "boolean",
                    "fa_icon": "fas fa-filter",
                    "default": true,
                    "description": "Enable filtering of amplicons with UMI sequences that show similarity to the LBS sequence."
                },
                "pna_amplicon_lbs_filter_min_overlap": {
                    "type": "integer",
                    "fa_icon": "fas fa-arrows-alt-h",
                    "default": 8,
                    "minimum": 4,
                    "maximum": 28,
                    "description": "The minimum overlap required in a semi-global alignment of a UMI sequence with the LBS regions. Reads with less overlap will not be removed by the LBS filter. [4<=x<=28]"
                },
                "pna_amplicon_lbs_filter_error_rate": {
                    "type": "number",
                    "fa_icon": "fas fa-percentage",
                    "default": 0.1,
                    "minimum": 0,
                    "maximum": 1,
                    "description": "The allowed error-rate in a semi-global alignment of a UMI sequence with the LBS regions. The error rate is defined as a percentage of UMI length. [0.0<=x<=1.0]"
                }
            }
        },
        "pna_demux_options": {
            "title": "Demux options",
            "type": "object",
            "fa_icon": "fas fa-random",
            "properties": {
                "pna_demux_mismatches": {
                    "fa_icon": "fas fa-not-equal",
                    "description": "The number of mismatches allowed in marker barcodes.",
                    "type": "integer",
                    "default": 1,
                    "minimum": 0,
                    "maximum": 2
                },
                "pna_demux_output_chunk_reads": {
                    "fa_icon": "fas fa-arrows-alt-h",
                    "type": "string",
                    "default": "50M",
                    "description": "The target number of reads in a single file of the partitioned demux output.",
                    "help": "This option can be used to fine-tune the parallelization of the subsequent collapse stage. A smaller value will create split the demux molecule list into more and smaller parts."
                },
                "pna_demux_output_max_chunks": {
                    "fa_icon": "fas fa-arrows-alt-h",
                    "type": "integer",
                    "minimum": 1,
                    "maximum": 32,
                    "default": 8,
                    "description": "The maximum number of chunks that the demuxed ouput for each umi region will be split into",
                    "help": "This option is used to control the parallelization of the subsequent collapse stage."
                },
                "pna_demux_strategy": {
                    "fa_icon": "fas fa-code-branch",
                    "description": "The demux and collapsing strategy to use",
                    "default": "independent",
                    "enum": ["paired", "independent"],
                    "type": "string",
                    "help": "**paired:** Use the paired collapsing strategy. This is the default and recommended strategy for PNA data.\n\n**independent:** Use the independent collapsing strategy. This strategy will corrects errors in UMI regions independently. It provides performance benefits but is experimental."
                },
                "save_pna_demux_parquet": {
                    "fa_icon": "fas fa-save",
                    "type": "boolean",
                    "description": "Save intermediate parquet files containing embeddings of all reads that contain valid antibody barcodes.",
                    "help": "By default, parquet files containing embeddings of reads with valid antibody barcodes will not be saved to the results directory. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete."
                },
                "save_pna_demux_passed_reads": {
                    "fa_icon": "fas fa-save",
                    "type": "boolean",
                    "description": "Save intermediate FASTQC read files containing all reads that contain valid antibody barcodes.",
                    "help": "By default, FastQ files containing reads with valid antibody barcodes will not be saved to the results directory. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete."
                },
                "save_pna_demux_failed_reads": {
                    "fa_icon": "fas fa-save",
                    "type": "boolean",
                    "description": "Save intermediate FASTQC read files containing all reads that do not contain valid antibody barcodes.",
                    "help": "By default, FastQ files containing reads without valid antibody barcodes will not be saved to the results directory. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete."
                }
            }
        },
        "pna_collapse_options": {
            "title": "Collapse options",
            "type": "object",
            "fa_icon": "fas fa-compress-alt",
            "properties": {
                "pna_collapse_algorithm": {
                    "fa_icon": "fas fa-project-diagram",
                    "description": "The algorithm to use for collapsing.",
                    "default": "directional",
                    "enum": ["cluster", "directional"],
                    "type": "string",
                    "help": "**cluster:** Form networks of connected UMIs (based on hamming distance threshold). Each connected component is a read group. In the above example, all the UMIs are contained in a single connected component and thus there is one read group containing all reads, with ACGT as the `selected` UMI.\n\n**directional (default):** Form networks with edges defined based on hamming distance threshold and node A counts >= (2 * node B counts) - 1. Each connected component is a read group, with the node with the highest counts selected as the top node for the component."
                },
                "pna_collapse_mismatches": {
                    "fa_icon": "fas fa-not-equal",
                    "description": "The number of mismatches allowed when collapsing (adjacency)",
                    "type": "integer",
                    "default": 2,
                    "minimum": 0,
                    "maximum": 5
                },
                "save_pna_collapsed_reads": {
                    "fa_icon": "fas fa-save",
                    "type": "boolean",
                    "description": "Save an intermediate parquet file containing collapsed read information.",
                    "help": "By default, intermediate collapsed reads will not be saved to the results directory. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete."
                }
            }
        },
        "pna_graph_options": {
            "title": "Graph options",
            "type": "object",
            "fa_icon": "fas fa-project-diagram",
            "properties": {
                "save_pna_graph_pixelfile": {
                    "type": "boolean",
                    "fa_icon": "fas fa-save",
                    "description": "Save the PXL dataset after the graph stage.",
                    "help": "By default, the PXL file after graph will not be saved to the results directory unless `--skip_analysis` and `--skip_layout` is passed. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete."
                },
                "pna_graph_multiplet_recovery": {
                    "description": "Activate the multiplet recovery using leiden community detection",
                    "fa_icon": "fas fa-project-diagram",
                    "type": "boolean",
                    "default": true
                },
                "pna_graph_initial_stage_leiden_resolution": {
                    "default": 1.0,
                    "fa_icon": "fas fa-sliders-h",
                    "minimum": 0,
                    "type": "number",
                    "description": "The resolution parameter for the leiden algorithm at the initial stage.",
                    "help": "This should typically be set higher than the refinement stage resolution."
                },
                "pna_graph_refinement_stage_leiden_resolution": {
                    "default": 0.01,
                    "fa_icon": "fas fa-sliders-h",
                    "minimum": 0,
                    "type": "number",
                    "description": "The resolution parameter for the leiden algorithm at the refinement stage.",
                    "help": "This should typically be set lower than the initial stage resolution."
                },
                "pna_graph_edge_cycle_verification": {
                    "type": "boolean",
                    "fa_icon": "fas fa-check-circle",
                    "default": true,
                    "description": "Activate edge cycle verification to remove edges from well connected regions that are not part of cycles in the graph.",
                    "help": "This option can help improve the quality of the graph by removing potentially false edges."
                },
                "pna_graph_min_count": {
                    "default": 1.0,
                    "fa_icon": "fas fa-hashtag",
                    "maximum": 50,
                    "minimum": 0,
                    "type": "number",
                    "description": "Discard edges with a read count below given value. Set to 1 to disable filtering."
                },
                "pna_graph_max_refinement_recursion_depth": {
                    "type": "integer",
                    "fa_icon": "fas fa-sitemap",
                    "default": 3,
                    "minimum": 1,
                    "maximum": 100,
                    "description": "The maximum recursion depth for the refinement algorithm. Set to 1 to disable refinement."
                },
                "pna_graph_initial_stage_max_edges_to_remove": {
                    "type": "integer",
                    "fa_icon": "fas fa-trash",
                    "default": 10,
                    "minimum": 1,
                    "description": "The maximum number of edges to remove between components during the initial stage (iteration == 0) of multiplet recovery."
                },
                "pna_graph_refinement_stage_max_edges_to_remove": {
                    "type": "integer",
                    "fa_icon": "fas fa-trash",
                    "default": 10,
                    "minimum": 1,
                    "description": "The maximum number of edges to remove between components during the refinement stage (iteration > 0) of multiplet recovery."
                },
                "pna_graph_initial_stage_max_edges_to_remove_relative": {
                    "type": "number",
                    "fa_icon": "fas fa-trash",
                    "minimum": 0,
                    "description": "The maximum number of edges to remove between two components relative to the number of nodes in the smaller of the two when during the initial stage (iteration == 0) of multiplet recovery."
                },
                "pna_graph_refinement_stage_max_edges_to_remove_relative": {
                    "type": "number",
                    "fa_icon": "fas fa-trash",
                    "minimum": 0,
                    "description": "The maximum number of edges to remove between two components relative to the number of nodes in the smaller of the two when during the refinement stage (iteration > 0) of multiplet recovery."
                },
                "pna_graph_component_size_min_threshold": {
                    "type": "integer",
                    "fa_icon": "fas fa-expand-alt",
                    "minimum": 1,
                    "default": 8000,
                    "description": "Components with fewer nodes than this will be filtered from the output data. Set to null to enable automatic size filtering based on the data."
                }
            }
        },
        "pna_sample_calling_options": {
            "title": "Sample calling options",
            "type": "object",
            "fa_icon": "fas fa-vial",
            "properties": {
                "save_pna_sample_calling_pixelfile": {
                    "type": "boolean",
                    "fa_icon": "fas fa-save",
                    "description": "Save the PXL dataset after the sample calling stage.",
                    "help": "By default, the PXL file after sample calling will not be saved to the results directory. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete."
                },
                "pna_sample_calling_save_undetermined": {
                    "type": "boolean",
                    "fa_icon": "fas fa-save",
                    "description": "Save components that could not be confidently assigned to any sample to a separate pxl file."
                },
                "pna_sample_calling_remove_incompatible": {
                    "type": "boolean",
                    "fa_icon": "fas fa-trash",
                    "description": "Remove antibodies that are incompatible with their component's called sample.",
                    "default": true
                },
                "pna_sample_calling_confidence_threshold": {
                    "type": "number",
                    "fa_icon": "fas fa-percentage",
                    "description": "Confidence threshold for sample calling.",
                    "help_text": "Components with a sample confidence below this threshold will be considered undetermined.",
                    "default": 0.9,
                    "minimum": 0.0,
                    "maximum": 1.0
                }
            }
        },
        "pna_denoise_options": {
            "title": "Denoise options",
            "type": "object",
            "fa_icon": "fas fa-microscope",
            "properties": {
                "skip_denoise": {
                    "description": "Skip denoise step",
                    "fa_icon": "fas fa-forward",
                    "type": "boolean"
                },
                "save_pna_denoise_pixelfile": {
                    "fa_icon": "fas fa-save",
                    "type": "boolean",
                    "description": "Save the PXL dataset after the denoise stage.",
                    "help": "By default, the PXL file after denoise will not be saved to the results directory."
                },
                "pna_denoise_run_one_core_graph_denoising": {
                    "description": "Activate the one-core graph denoising algorithm",
                    "fa_icon": "fas fa-microscope",
                    "type": "boolean"
                },
                "pna_denoise_pval_threshold": {
                    "type": "number",
                    "fa_icon": "fas fa-flask",
                    "description": "The p-value threshold for the a marker to be considered significantly over-expressed in the one-core layer of a component",
                    "default": 0.05,
                    "minimum": 0
                },
                "pna_denoise_inflate_factor": {
                    "type": "number",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "description": "The inflate factor for the number of nodes from over-expressed markers to be removed from the one-core layer of a component",
                    "default": 1.5,
                    "minimum": 1
                },
                "pna_denoise_run_ace_denoising": {
                    "type": "boolean",
                    "fa_icon": "fas fa-microscope",
                    "description": "Remove nodes in the peripheral-like partition using adaptive core expansion (ACE).",
                    "default": true
                },
                "pna_denoise_ace_k": {
                    "type": "integer",
                    "description": "Neighborhood radius in graph steps for ACE denoising.",
                    "fa_icon": "far fa-circle",
                    "default": 3,
                    "minimum": 1,
                    "maximum": 6
                },
                "pna_denoise_run_pls_denoising": {
                    "type": "boolean",
                    "fa_icon": "fas fa-microscope",
                    "description": "Run PLS-on-coreness denoising and retain the largest connected component after filtering.",
                    "default": true
                },
                "pna_denoise_pls_score_threshold": {
                    "type": "number",
                    "description": "All retained PLS score columns must exceed this value.",
                    "fa_icon": "fas fa-less-than-equal",
                    "default": -3.0
                }
            }
        },
        "pna_analysis_options": {
            "title": "Analysis options",
            "type": "object",
            "fa_icon": "fas fa-chart-line",
            "properties": {
                "skip_analysis": {
                    "description": "Skip analysis step",
                    "fa_icon": "fas fa-forward",
                    "type": "boolean"
                },
                "save_pna_analysis_pixelfile": {
                    "fa_icon": "fas fa-save",
                    "type": "boolean",
                    "description": "Save the PXL dataset after the analysis stage.",
                    "help": "By default, the PXL dataset after the analysis stage will only be saved be saved when `--skip_layout` is passed. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete."
                },
                "pna_analysis_compute_proximity": {
                    "description": "Compute proximity scores",
                    "fa_icon": "fas fa-ruler-combined",
                    "type": "boolean",
                    "default": true
                },
                "pna_analysis_compute_k_cores": {
                    "description": "Compute k-core summary tables for each component",
                    "fa_icon": "fas fa-network-wired",
                    "type": "boolean",
                    "default": true
                },
                "pna_analysis_proximity_nbr_of_permutations": {
                    "type": "integer",
                    "fa_icon": "fas fa-random",
                    "description": "Number of permutations to use when computing the expected proximity scores",
                    "default": 100,
                    "minimum": 50
                },
                "pna_analysis_compute_svd_var_explained": {
                    "description": "Compute the variance explained by the SVD components",
                    "fa_icon": "fas fa-chart-pie",
                    "type": "boolean",
                    "default": true
                },
                "pna_analysis_svd_nbr_of_pivots": {
                    "type": "integer",
                    "fa_icon": "fas fa-compass",
                    "description": "Number of pivots to use for the SVD decomposition",
                    "default": 50,
                    "minimum": 10,
                    "maximum": 200
                }
            }
        },
        "pna_layout_options": {
            "title": "Layout options",
            "type": "object",
            "fa_icon": "fas fa-draw-polygon",
            "properties": {
                "skip_layout": {
                    "description": "Skip layout step",
                    "fa_icon": "fas fa-forward",
                    "type": "boolean"
                },
                "pna_layout_no_node_marker_counts": {
                    "description": "Skip adding marker counts to the layout.",
                    "fa_icon": "fas fa-ban",
                    "type": "boolean"
                },
                "pna_layout_layout_algorithm": {
                    "description": "Select a layout algorithm to use. This can be specified as a comma separated list to compute multiple layouts. Possible values are: pmds, pmds_3d, wpmds, wpmds_3d.",
                    "fa_icon": "fas fa-project-diagram",
                    "type": "string",
                    "enum": ["pmds_3d", "wpmds_3d"],
                    "default": "wpmds_3d"
                },
                "pna_layout_pmds_pivots": {
                    "type": "integer",
                    "fa_icon": "fas fa-compass",
                    "description": "Number of pivots to use for the PMDS layout algorithm. Default: 50. More gives better results, but increases computation time.",
                    "default": 50,
                    "minimum": 50
                },
                "pna_layout_wpmds_k": {
                    "type": "integer",
                    "fa_icon": "fas fa-ruler",
                    "description": "The window size used when computing probability weights for the wpmds layout method. Only used when layout algorithm is set to wpmds.",
                    "default": 5,
                    "minimum": 1,
                    "maximum": 10
                }
            }
        },
        "experiment_summary_options": {
            "title": "Experiment Summary options",
            "type": "object",
            "fa_icon": "fas fa-clipboard-list",
            "properties": {
                "skip_experiment_summary": {
                    "description": "Skip experiment summary generation",
                    "fa_icon": "fas fa-forward",
                    "type": "boolean"
                }
            }
        },
        "global_config_options": {
            "title": "Global options",
            "type": "object",
            "fa_icon": "fas fa-cogs",
            "description": "Global configuration options specific to nf-core/pixelator.",
            "required": ["technology"],
            "properties": {
                "pixelator_container": {
                    "type": "string",
                    "fa_icon": "fas fa-box",
                    "description": "Override the container image reference to use for all steps using the `pixelator` command.",
                    "help_text": "Use this to force the pipeline to use a different image version in all steps that use the pixelator command.\nThe pipeline is not guaranteed to work when using different pixelator versions."
                },
                "experiment_summary_container": {
                    "type": "string",
                    "fa_icon": "fas fa-box",
                    "description": "Override the container image to use for the experiment summary step.",
                    "help_text": "Use this to force the pipeline to use a different image version for the experiment summary step.\nThe pipeline is not guaranteed to work when using different experiment summary versions."
                },
                "save_all": {
                    "fa_icon": "fas fa-save",
                    "type": "boolean",
                    "description": "Save all intermediate results.",
                    "help": "This option is equivalent of passing all: `--save_* and --save_pna_*` options."
                },
                "save_json": {
                    "fa_icon": "fas fa-save",
                    "type": "boolean",
                    "default": true,
                    "description": "Save all JSON report and metadata files generated by pixelator."
                },
                "technology": {
                    "type": "string",
                    "fa_icon": "fas fa-microchip",
                    "description": "The technology used to process the samples",
                    "enum": ["proxiome-v1", "proxiome-v2", "hashed_samples", "nonhashed_samples"]
                }
            }
        },
        "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
                },
                "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
                },
                "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/pixelator/",
                    "hidden": true
                },
                "modules_testdata_base_path": {
                    "type": "string",
                    "description": "Base path / URL for data used in the modules",
                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/",
                    "hidden": true
                },
                "trace_report_suffix": {
                    "type": "string",
                    "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/pna_amplicon_options"
        },
        {
            "$ref": "#/$defs/pna_demux_options"
        },
        {
            "$ref": "#/$defs/pna_collapse_options"
        },
        {
            "$ref": "#/$defs/pna_graph_options"
        },
        {
            "$ref": "#/$defs/pna_sample_calling_options"
        },
        {
            "$ref": "#/$defs/pna_denoise_options"
        },
        {
            "$ref": "#/$defs/pna_analysis_options"
        },
        {
            "$ref": "#/$defs/pna_layout_options"
        },
        {
            "$ref": "#/$defs/experiment_summary_options"
        },
        {
            "$ref": "#/$defs/global_config_options"
        },
        {
            "$ref": "#/$defs/institutional_config_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        }
    ]
}