{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/airrflow/master/nextflow_schema.json",
    "title": "nf-core/airrflow pipeline parameters",
    "description": "B and T cell repertoire analysis pipeline with the Immcantation framework.",
    "type": "object",
    "$defs": {
        "input_output_options": {
            "title": "Input output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": ["input", "outdir"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_input.json",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.tsv$",
                    "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/airrflow/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "mode": {
                    "type": "string",
                    "default": "fastq",
                    "description": "Specify the processing mode for the pipeline. Available options are \"fastq\" and \"assembled\".",
                    "enum": ["fastq", "assembled"],
                    "fa_icon": "fas fa-terminal"
                },
                "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})$"
                },
                "miairr": {
                    "type": "string",
                    "default": "${projectDir}/assets/reveal/mapping_MiAIRR_BioSample_v1.3.1.tsv",
                    "description": "Path to MiAIRR-BioSample mapping",
                    "fa_icon": "fas fa-table"
                }
            }
        },
        "protocol": {
            "title": "Protocol",
            "type": "object",
            "description": "Experimental protocol used to generate the data",
            "default": "",
            "properties": {
                "library_generation_method": {
                    "type": "string",
                    "fa_icon": "fas fa-flask",
                    "description": "Protocol used for the V(D)J amplicon sequencing library generation.",
                    "enum": [
                        "specific_pcr_umi",
                        "specific_pcr",
                        "dt_5p_race",
                        "dt_5p_race_umi",
                        "sc_10x_genomics",
                        "trust4"
                    ],
                    "help_text": "Available protocols are:\n- `specific_pcr_umi`: RT-PCR using transcript-specific primers containing UMIs.\n- `specific_pcr`: RT-PCR using transcript-specific primers.\n- `dt_5p_race_umi`: 5\u2019-RACE PCR using oligo-dT primers and template switch primers containing UMI.\n- `dt_5p_race`: 5\u2019-RACE PCR (i.e. RT is followed by a template switch (TS) step) using oligo-dT primers.\n- `sc_10x_genomics`:10x genomics library preparation protocol for scVDJ sequencing."
                },
                "race_linker": {
                    "type": "string",
                    "description": "Path to fasta file containing the linker sequence, if no V-region primers were used but a linker sequence is present (e.g. 5' RACE SMARTer TAKARA protocol).",
                    "fa_icon": "fas fa-dna"
                }
            },
            "fa_icon": "fas fa-flask"
        },
        "primer_input_and_positions": {
            "title": "Primer input and positions",
            "type": "object",
            "description": "Define the primer region start and how to deal with the primer alignment.",
            "default": "",
            "properties": {
                "vprimers": {
                    "type": "string",
                    "fa_icon": "fas fa-dna",
                    "description": "Path to a fasta file containinc the V-region primer sequences."
                },
                "cprimers": {
                    "type": "string",
                    "fa_icon": "fas fa-dna",
                    "description": "Path to a fasta file containing the C-region primer sequences."
                },
                "vprimer_start": {
                    "type": "integer",
                    "description": "Start position of V region primers (without counting the UMI barcode).",
                    "fa_icon": "fas fa-dna",
                    "default": 0
                },
                "cprimer_start": {
                    "type": "integer",
                    "description": "Start position of C region primers (without counting the UMI barcode).",
                    "fa_icon": "fas fa-dna",
                    "default": 0
                },
                "cprimer_position": {
                    "type": "string",
                    "default": "R1",
                    "fa_icon": "fas fa-dna",
                    "description": "Indicate if C region primers are in the R1 or R2 reads.",
                    "enum": ["R1", "R2"]
                },
                "primer_revpr": {
                    "type": "boolean",
                    "description": "Specify to match the tail-end of the sequence against the reverse complement of the primers. This also reverses the behavior of the --start argument, such that start position is relative to the tail-end of the sequence. (default: False)Maximum scoring error for the Presto MaxPrimer process for the C and/or V region primers identification.",
                    "fa_icon": "fas fa-dna"
                }
            },
            "fa_icon": "fas fa-dna"
        },
        "umi_barcode_handling": {
            "title": "UMI barcode handling",
            "type": "object",
            "description": "Define how UMI barcodes should be treated.",
            "default": "",
            "properties": {
                "umi_position": {
                    "type": "string",
                    "default": "R1",
                    "description": "Indicate if UMI indices are recorded in the R1 (default) or R1 fastq file.",
                    "help_text": "The pipeline requires UMI barcodes for identifying unique transcripts. These barcodes are typically read from an index file but sometimes can be provided merged with the start of the R1 or R2 reads. If provided in an additional index file, set the `--index_file` parameter, if provided merged with the R1 or R2 reads, set the `--umi_position` parameter to R1 or R2, respectively.",
                    "enum": ["R1", "R2"],
                    "fa_icon": "fas fa-barcode"
                },
                "umi_length": {
                    "type": "integer",
                    "description": "UMI barcode length in nucleotides. Set to 0 if no UMIs present.",
                    "fa_icon": "fas fa-barcode",
                    "default": -1
                },
                "umi_start": {
                    "type": "integer",
                    "description": "UMI barcode start position in the index read.",
                    "fa_icon": "fas fa-barcode",
                    "default": 0
                },
                "index_file": {
                    "type": "boolean",
                    "description": "Indicate if UMI indices are recorded in a separate index file.",
                    "help_text": "Set to `true` if UMI barcodes are to be read from a separate Illumina index fastq file. If Illumina indices and UMI barcodes are already integrated into the R1 reads, leave the default `--index_file false`.\n\nThe pipeline requires UMI barcodes for identifying unique transcripts. These barcodes are typically read from an index file but sometimes can be provided merged with the start of the R1 or R2 reads. If provided in an additional index file, set the `--index_file` parameter, if provided merged with the R1 or R2 reads, set the `--umi_position` parameter.",
                    "fa_icon": "fas fa-barcode"
                }
            },
            "help_text": "The pipeline requires indication of UMI barcode treatment (for identifying unique transcripts). These barcodes are typically read from an index file but sometimes can be provided merged with the start of the R1 or R2 reads. If provided in an additional index file, set the `--index_file` parameter, if provided merged with the R1 or R2 reads, set the `--umi_position` parameter. Specify the UMI barcode length with the `--umi_length` parameter. If no UMI barcodes are present, specify `--umi_length = 0` to use the sans-UMI subworkflow.",
            "fa_icon": "fas fa-barcode"
        },
        "adapter_trimming": {
            "title": "Adapter trimming",
            "type": "object",
            "description": "Options for adapter trimming and read clipping",
            "default": "",
            "fa_icon": "fas fa-cut",
            "properties": {
                "trim_fastq": {
                    "type": "boolean",
                    "default": true,
                    "description": "Whether to trim adapters in fastq reads with fastp.",
                    "help_text": "By default adapters will be auto-detected, but adapter sequences can also be provided in a `fasta` file with the `--adapter_fasta` option.",
                    "fa_icon": "fas fa-cut"
                },
                "adapter_fasta": {
                    "type": "string",
                    "fa_icon": "fas fa-file",
                    "description": "Fasta file with adapter sequences to be trimmed."
                },
                "clip_r1": {
                    "type": "integer",
                    "default": 0,
                    "description": "Number of bases to clip 5' in R1 reads.",
                    "fa_icon": "fas fa-cut"
                },
                "clip_r2": {
                    "type": "integer",
                    "default": 0,
                    "description": "Number of bases to clip 5' in R2 reads.",
                    "fa_icon": "fas fa-cut"
                },
                "three_prime_clip_r1": {
                    "type": "integer",
                    "default": 0,
                    "description": "Number of bases to clip 3' in R1 reads.",
                    "fa_icon": "fas fa-cut"
                },
                "three_prime_clip_r2": {
                    "type": "integer",
                    "default": 0,
                    "description": "Number of bases to clip 3' in R2 reads.",
                    "fa_icon": "fas fa-cut"
                },
                "trim_nextseq": {
                    "type": "boolean",
                    "description": "Trim adapters specific for Nextseq sequencing",
                    "fa_icon": "fas fa-cut"
                },
                "save_trimmed": {
                    "type": "boolean",
                    "description": "Option to save trimmed reads.",
                    "fa_icon": "far fa-save"
                }
            }
        },
        "sequence_assembly_options": {
            "title": "Sequence Assembly options",
            "type": "object",
            "description": "Options for the pRESTO sequence assembly processes",
            "default": "",
            "properties": {
                "filterseq_q": {
                    "type": "integer",
                    "default": 20,
                    "description": "Quality threshold for pRESTO FilterSeq sequence filtering.",
                    "fa_icon": "fas fa-filter"
                },
                "primer_consensus": {
                    "type": "number",
                    "default": 0.6,
                    "description": "Maximum error for building the primer consensus in the pRESTO Buildconsensus step.",
                    "fa_icon": "fas fa-align-left"
                },
                "buildconsensus_maxerror": {
                    "type": "number",
                    "default": 0.1,
                    "fa_icon": "fas fa-align-center",
                    "description": "Maximum error for building the sequence consensus in the pRESTO BuildConsensus step."
                },
                "buildconsensus_maxgap": {
                    "type": "number",
                    "default": 0.5,
                    "fa_icon": "fas fa-align-center",
                    "description": "Maximum gap for building the sequence consensus in the pRESTO BuildConsensus step."
                },
                "cluster_sets": {
                    "type": "boolean",
                    "default": true,
                    "fa_icon": "fas fa-align-center",
                    "description": "Cluster sequences by similarity regardless of any annotation with pRESTO ClusterSets and annotate the cluster ID additionally to the UMI barcode."
                },
                "primer_r1_maxerror": {
                    "type": "number",
                    "default": 0.2,
                    "fa_icon": "fas fa-align-left",
                    "description": "Maximum allowed error for R1 primer alignment."
                },
                "primer_r2_maxerror": {
                    "type": "number",
                    "default": 0.2,
                    "fa_icon": "fas fa-align-right",
                    "description": "Maximum allowed error for R2 primer alignment."
                },
                "maskprimers_align": {
                    "type": "boolean",
                    "fa_icon": "fas fa-align-center",
                    "description": "Align primers instead of scoring them. Used for protocols without primer fixed positions."
                },
                "primer_maxlen": {
                    "type": "integer",
                    "default": 50,
                    "fa_icon": "fas fa-align-center",
                    "description": "Maximum allowed primer length when aligning the primers."
                },
                "primer_r1_mask_mode": {
                    "type": "string",
                    "fa_icon": "fas fa-mask",
                    "description": "Masking mode for R1 primers.",
                    "enum": ["cut", "mask", "trim", "tag"],
                    "default": "cut",
                    "help_text": "See [pRESTO MaskPrimers](https://presto.readthedocs.io/en/stable/tools/MaskPrimers.html) for more information."
                },
                "primer_r2_mask_mode": {
                    "type": "string",
                    "default": "cut",
                    "fa_icon": "fas fa-mask",
                    "enum": ["cut", "mask", "trim", "tag"],
                    "description": "Masking mode for R2 primers.",
                    "help_text": "See [pRESTO MaskPrimers](https://presto.readthedocs.io/en/stable/tools/MaskPrimers.html) for more information."
                },
                "maskprimers_align_race": {
                    "type": "boolean",
                    "fa_icon": "fas fa-align-center",
                    "description": "Use MaskPrimers align for a 5' RACE protocol.",
                    "help_text": "It will align the C-primers with pRESTO MaskPrimers align, and extract the template-switch Oligo and/or linker with defined length in `--primer_r2_extract_len`."
                },
                "maskprimers_extract": {
                    "type": "boolean",
                    "fa_icon": "fas fa-cut",
                    "description": "Use when primer sequences are unknown but when their approximate positions are known.",
                    "help_text": "Use in combination with `--primer_r1_extract_len` and `--primer_r2_extract_len` to define the sequence regions to cut corresponding to the approximate unknown primer sequence length prior to alignment. It is also possible to define a UMI barcode for extraction if it's position is unknown."
                },
                "primer_r1_extract_len": {
                    "type": "integer",
                    "default": 0,
                    "fa_icon": "fas fa-cut",
                    "description": "R1 primer extract length when using `--maskprimers_extract`."
                },
                "primer_r2_extract_len": {
                    "type": "integer",
                    "default": 0,
                    "fa_icon": "fas fa-cut",
                    "description": "R2 primer extract length when using `--maskprimers_extract`."
                },
                "assemblepairs_sequential": {
                    "type": "boolean",
                    "fa_icon": "fas fa-align-center",
                    "description": "Use AssemblePairs sequential instead of AssemblePairs align when assembling read pairs."
                },
                "align_cregion": {
                    "type": "boolean",
                    "fa_icon": "fas fa-align-center",
                    "description": "Align internal C-region for a more precise isotype characterization."
                },
                "internal_cregion_sequences": {
                    "type": "string",
                    "fa_icon": "fas fa-align-center",
                    "description": "Provide internal C-region sequences for a more precise C-region characterization. Then also set the `align_cregion` flag."
                },
                "cregion_maxlen": {
                    "type": "integer",
                    "default": 100,
                    "fa_icon": "fas fa-align-center",
                    "description": "Maximum allowed length when aligning the internal C-region."
                },
                "cregion_maxerror": {
                    "type": "number",
                    "default": 0.3,
                    "fa_icon": "fas fa-align-center",
                    "description": "Maximum allowed error when aligning the internal C-region."
                },
                "cregion_mask_mode": {
                    "type": "string",
                    "default": "tag",
                    "fa_icon": "fas fa-mask",
                    "description": "Mask mode for C-region alignment."
                },
                "skip_alignment_filter": {
                    "type": "boolean",
                    "fa_icon": "fas fa-fast-forward",
                    "description": "Skip filter step after alignment that ensures that locus should match the v_call chain, the sequence alignment should have at least 200 informative positions (excluding N or gaps), and maximum 10% N nucleotides in the alignment."
                }
            },
            "fa_icon": "fas fa-align-center"
        },
        "vdj_annotation_options": {
            "title": "VDJ annotation options",
            "type": "object",
            "description": "Options for the VDJ annotation processes.",
            "default": "",
            "properties": {
                "reassign": {
                    "type": "boolean",
                    "default": true,
                    "description": "Whether to reassign genes if the input file is an AIRR formatted tabulated file.",
                    "fa_icon": "fas fa-redo"
                },
                "productive_only": {
                    "type": "boolean",
                    "default": true,
                    "description": "Subset to productive  sequences.",
                    "fa_icon": "fab fa-product-hunt"
                },
                "save_databases": {
                    "type": "boolean",
                    "description": "Save databases so you can use the cache in future runs.",
                    "fa_icon": "fas fa-file-download",
                    "default": true
                },
                "reference_fasta": {
                    "type": "string",
                    "description": "Path to the germline reference fasta.",
                    "help_text": "By default, we provide a pre-downloaded version of the IMGT database. It is also possible to provide a custom reference fasta database. To fetch a fresh version of IMGT, set the `--fetch_imgt` parameter instead.",
                    "fa_icon": "fas fa-database",
                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip"
                },
                "reference_igblast": {
                    "type": "string",
                    "description": "Path to the cached igblast database.",
                    "help_text": "By default, we provide a pre-downloaded version of the IMGT database. It is also possible to provide a custom reference fasta database. To fetch a fresh version of IMGT, set the `--fetch_imgt` parameter instead.",
                    "fa_icon": "fas fa-database",
                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip"
                },
                "fetch_imgt": {
                    "type": "boolean",
                    "description": "Set this flag to fetch the IMGT reference data at runtime.",
                    "fa_icon": "fas fa-cloud-download-alt"
                }
            },
            "fa_icon": "fas fa-edit"
        },
        "bulk_filtering_options": {
            "title": "Bulk filtering options",
            "type": "object",
            "description": "Options for bulk sequence filtering after VDJ assignment.",
            "default": "",
            "properties": {
                "collapseby": {
                    "type": "string",
                    "description": "Name of the field used to collapse duplicated sequences.",
                    "fa_icon": "fas fa-compress-alt",
                    "default": "sample_id"
                },
                "detect_contamination": {
                    "type": "boolean",
                    "fa_icon": "fas fa-search",
                    "description": "Whether to run the process to detect contamination."
                },
                "remove_chimeric": {
                    "type": "boolean",
                    "description": "Whether to apply the chimera removal filter.",
                    "fa_icon": "fas fa-minus-square"
                }
            },
            "fa_icon": "fas fa-filter"
        },
        "clonal_analysis_options": {
            "title": "Clonal analysis options",
            "type": "object",
            "description": "Define how the B-cell clonal trees should be calculated.",
            "default": "",
            "properties": {
                "clonal_threshold": {
                    "oneOf": [
                        {
                            "type": "string",
                            "enum": ["auto"]
                        },
                        {
                            "type": "number",
                            "minimum": 0
                        }
                    ],
                    "type": ["string", "number"],
                    "default": "auto",
                    "fa_icon": "fab fa-pagelines",
                    "description": "Set the clustering threshold Hamming distance value. Default: 'auto'"
                },
                "lineage_trees": {
                    "type": "boolean",
                    "description": "Perform clonal lineage tree analysis.",
                    "fa_icon": "fas fa-angle-double-right"
                },
                "cloneby": {
                    "type": "string",
                    "default": "subject_id",
                    "description": "Name of the field used to group data files to identify clones.",
                    "fa_icon": "fab fa-pagelines"
                },
                "crossby": {
                    "type": "string",
                    "default": "subject_id",
                    "description": "Name of the field used to identify external groups used to identify a clonal threshold.",
                    "fa_icon": "fab fa-pagelines"
                },
                "lineage_tree_builder": {
                    "type": "string",
                    "default": "raxml",
                    "description": "Lineage tree software to use to build trees within Dowser. If you change the default, also set the `lineage_tree_exec` parameter.",
                    "enum": ["raxml", "igphyml"],
                    "fa_icon": "fab fa-pagelines"
                },
                "lineage_tree_exec": {
                    "type": "string",
                    "default": "/usr/local/bin/raxml-ng",
                    "description": "Path to lineage tree building executable.",
                    "fa_icon": "fab fa-pagelines"
                },
                "singlecell": {
                    "type": "string",
                    "default": "single_cell",
                    "description": "Name of the field used to determine if a sample is single cell sequencing or not.",
                    "fa_icon": "fas fa-border-all"
                },
                "skip_all_clones_report": {
                    "type": "boolean",
                    "description": "Skip report of EnchantR DefineClones for all samples together.",
                    "fa_icon": "fas fa-angle-double-right"
                },
                "skip_report_threshold": {
                    "type": "boolean",
                    "description": "Skip report of EnchantR FindThreshold for all samples together.",
                    "fa_icon": "fas fa-angle-double-right"
                }
            },
            "help_text": "By default, the pipeline will define clones for each of the samples, as two sequences having the same V-gene assignment, C-gene assignment, J-gene assignment, and junction length. Additionally, the similarity of the CDR3 sequences will be assessed by Hamming distances. \n\nA distance threshold for determining if two sequences come from the same clone or not is automatically determined by the process find threshold. Alternatively, a hamming distance threshold can be  manually set by setting the `--clonal_threshold` parameter.",
            "fa_icon": "fab fa-pagelines"
        },
        "single_cell_analysis_options": {
            "title": "Single cell analysis options",
            "type": "object",
            "description": "Options specific for raw single cell input.",
            "default": "",
            "properties": {
                "reference_10x": {
                    "type": "string",
                    "description": "Path to the reference directory required by cellranger. Can either be directory or tar.gz.",
                    "help_text": "See for [IMGT](https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references#imgt) or [default](https://www.10xgenomics.com/support/software/cell-ranger/downloads).",
                    "fa_icon": "fas fa-database"
                }
            },
            "help_text": "Options for running raw single cell data.",
            "fa_icon": "fab fa-pagelines"
        },
        "rnaseq_based_analysis_options": {
            "title": "Unselected RNA-seq based analysis options",
            "type": "object",
            "description": "Options specific for raw unselected RNA-seq input.",
            "default": "",
            "properties": {
                "cell_barcode_read": {
                    "type": "string",
                    "description": "Specifies which read holds the barcodes",
                    "enum": ["R1", "R2"],
                    "fa_icon": "fas fa-terminal",
                    "help_text": "file containing the barcodes"
                },
                "umi_read": {
                    "type": "string",
                    "description": "Indicate if UMI indices are recorded in the R1 (default) or R1 fastq file.",
                    "help_text": "file containing 10x Genomics-like UMIs",
                    "enum": ["R1", "R2"],
                    "fa_icon": "fas fa-barcode"
                },
                "read_format": {
                    "type": "string",
                    "description": "Specifies where in the read the barcodes and UMIs can be found.",
                    "help_text": "For further information see the TRUST4 [docs](https://github.com/liulab-dfci/TRUST4?tab=readme-ov-file#10x-genomics-data-and-barcode-based-single-cell-data).",
                    "fa_icon": "fas fa-terminal"
                }
            },
            "help_text": "Options for running raw RNA seq data.",
            "fa_icon": "fab fa-pagelines"
        },
        "report_options": {
            "title": "Report options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "report_rmd": {
                    "type": "string",
                    "default": "${projectDir}/assets/repertoire_comparison.Rmd",
                    "description": "Custom report Rmarkdown file.",
                    "fa_icon": "far fa-file-code"
                },
                "report_css": {
                    "type": "string",
                    "default": "${projectDir}/assets/nf-core_style.css",
                    "description": "Custom report style file in css format.",
                    "fa_icon": "far fa-file-code"
                },
                "report_logo": {
                    "type": "string",
                    "default": "${projectDir}/assets/nf-core-airrflow_logo_light.png",
                    "description": "Custom logo for the report.",
                    "fa_icon": "far fa-file-code"
                },
                "report_logo_img": {
                    "type": "string",
                    "default": "${projectDir}/assets/nf-core-airrflow_logo_reports.png",
                    "description": "Custom logo for the EnchantR reports.",
                    "fa_icon": "far fa-file-code"
                },
                "skip_report": {
                    "type": "boolean",
                    "description": "Skip repertoire analysis and report generation.",
                    "fa_icon": "fas fa-angle-double-right"
                },
                "skip_multiqc": {
                    "type": "boolean",
                    "description": "Skip multiqc report.",
                    "fa_icon": "fas fa-angle-double-right"
                }
            },
            "fa_icon": "far fa-file-code"
        },
        "reference_genome_options": {
            "title": "Reference genome options",
            "type": "object",
            "fa_icon": "fas fa-dna",
            "description": "Options for the reference genome indices used to align reads.",
            "properties": {
                "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`.",
                    "default": true
                },
                "igenomes_base": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The base path to the igenomes reference files",
                    "fa_icon": "fas fa-ban",
                    "hidden": true,
                    "default": "s3://ngi-igenomes/igenomes/"
                }
            }
        },
        "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": "Directory to keep pipeline Nextflow logs and reports.",
                    "default": "${params.outdir}/pipeline_info",
                    "fa_icon": "fas fa-cogs",
                    "hidden": true
                }
            }
        },
        "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
                },
                "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"
                },
                "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
                },
                "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/airrflow/",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/$defs/input_output_options"
        },
        {
            "$ref": "#/$defs/protocol"
        },
        {
            "$ref": "#/$defs/primer_input_and_positions"
        },
        {
            "$ref": "#/$defs/umi_barcode_handling"
        },
        {
            "$ref": "#/$defs/adapter_trimming"
        },
        {
            "$ref": "#/$defs/sequence_assembly_options"
        },
        {
            "$ref": "#/$defs/vdj_annotation_options"
        },
        {
            "$ref": "#/$defs/bulk_filtering_options"
        },
        {
            "$ref": "#/$defs/clonal_analysis_options"
        },
        {
            "$ref": "#/$defs/single_cell_analysis_options"
        },
        {
            "$ref": "#/$defs/rnaseq_based_analysis_options"
        },
        {
            "$ref": "#/$defs/report_options"
        },
        {
            "$ref": "#/$defs/protocol"
        },
        {
            "$ref": "#/$defs/primer_input_and_positions"
        },
        {
            "$ref": "#/$defs/umi_barcode_handling"
        },
        {
            "$ref": "#/$defs/adapter_trimming"
        },
        {
            "$ref": "#/$defs/sequence_assembly_options"
        },
        {
            "$ref": "#/$defs/vdj_annotation_options"
        },
        {
            "$ref": "#/$defs/bulk_filtering_options"
        },
        {
            "$ref": "#/$defs/clonal_analysis_options"
        },
        {
            "$ref": "#/$defs/single_cell_analysis_options"
        },
        {
            "$ref": "#/$defs/rnaseq_based_analysis_options"
        },
        {
            "$ref": "#/$defs/report_options"
        },
        {
            "$ref": "#/$defs/reference_genome_options"
        },
        {
            "$ref": "#/$defs/institutional_config_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        }
    ]
}
