nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/number-25/LongTranscriptomics/refs/heads/dev/nextflow_schema.json",
    "title": "number-25/LongTranscriptomics pipeline parameters",
    "description": "Analysis pipeline for ONT directRNA sequencing data",
    "type": "object",
    "$defs": {
        "reference_genome_options": {
            "title": "Reference genome options",
            "type": "object",
            "description": "Options for reference genome and transcriptome files and indices.",
            "default": "",
            "properties": {
                "genome_fasta": {
                    "type": "string",
                    "description": "Path to reference genome fasta."
                },
                "genome_fasta_index": {
                    "type": "string",
                    "description": "Path to reference genome index."
                },
                "genome_fasta_sizes": {
                    "type": "string",
                    "description": "Path to reference genome sizes."
                },
                "genome_minimap2_index": {
                    "type": "string",
                    "description": "Path to reference genome minimap2 index."
                },
                "transcriptome_mapping": {
                    "type": "boolean",
                    "description": "Map to reference transcriptome instead of genome."
                },
                "transcriptome_fasta": {
                    "type": "string",
                    "description": "Path to transcriptome fasta sequence."
                },
                "transcriptome_fasta_index": {
                    "type": "string",
                    "description": "Path to transcriptome fasta index."
                },
                "transcriptome_minimap2_index": {
                    "type": "string",
                    "description": "Path to transcriptome minimap2 index."
                },
                "annotation_gtf": {
                    "type": "string",
                    "description": "Path to reference transcriptome annotation."
                },
                "skip_prepare_reference": {
                    "type": "boolean",
                    "description": "Skip the preparation of the reference files."
                }
            },
            "required": ["genome_fasta", "transcriptome_fasta", "annotation_gtf"],
            "fa_icon": "fas fa-book-open"
        },
        "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", "sequencing_type"],
            "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 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.",
                    "fa_icon": "fas fa-file-csv",
                    "default": "assets/samplesheet.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",
                    "default": "outputs"
                },
                "help": {
                    "type": "boolean",
                    "description": "Show the help message for the pipeline.",
                    "fa_icon": "fas fa-question-circle",
                    "help_text": "Welcome to LongTranscriptomics, I see you are seeking help, these are  a list of basic parameters."
                },
                "sequencing_type": {
                    "type": "string",
                    "default": "ont-drna",
                    "description": "Type of Oxford Nanopore library.",
                    "help_text": "Type of Oxford nanopore library. Either 'ont-drna' or 'ont-cdna'.",
                    "fa_icon": "fas fa-font"
                }
            }
        },
        "multiqc_options": {
            "title": "MultiQC options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "multiqc_config": {
                    "type": "string",
                    "description": "Custom config file to supply to MultiQC."
                },
                "multiqc_logo": {
                    "type": "string",
                    "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file."
                },
                "multiqc_methods_description": {
                    "type": "string",
                    "description": "Custom MultiQC yaml file containing HTML including a methods description."
                },
                "multiqc_title": {
                    "type": "string",
                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified."
                }
            }
        },
        "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
                },
                "email": {
                    "type": "string",
                    "fa_icon": "fas fa-envelope",
                    "description": "Email address for completion summary."
                },
                "plaintext_email": {
                    "type": "boolean",
                    "description": "Send plain-text email instead of HTML.",
                    "fa_icon": "fas fa-remove-format"
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette"
                },
                "publish_dir_mode": {
                    "type": "string",
                    "default": "copy",
                    "fa_icon": "fas fa-copy",
                    "description": "Method used to save pipeline results to output directory."
                },
                "hook_url": {
                    "type": "string",
                    "description": "Incoming Webhook URL for messaging service."
                },
                "config_profile_description": {
                    "type": "string",
                    "description": "Institutional config description."
                },
                "config_profile_name": {
                    "type": "string",
                    "description": "Institutional config name."
                },
                "custom_config_version": {
                    "type": "string",
                    "default": "dev",
                    "description": "Git commit id for Institutional configs"
                },
                "custom_config_base": {
                    "type": "string",
                    "description": "Base directory for Institutional configs.",
                    "default": "conf/base.config"
                },
                "config_profile_contact": {
                    "type": "string",
                    "description": "Institutional config contact information.",
                    "default": "deancombio@pm.me"
                },
                "config_profile_url": {
                    "type": "string",
                    "description": "Institutional config URL link."
                }
            }
        },
        "module_specific_options": {
            "title": "Module specific options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "bam_input": {
                    "type": "boolean",
                    "description": "Input files are prealigned in BAM format."
                },
                "skip_qc": {
                    "type": "boolean",
                    "description": "Skip initial fastq QC.",
                    "help_text": "This skips all of the initial fastq QC, and is typically not recommended to skip."
                },
                "skip_nanoq": {
                    "type": "boolean",
                    "description": "Skip nano fastq QC."
                },
                "skip_sequali": {
                    "type": "boolean",
                    "description": "Skip sequali fastq QC."
                },
                "skip_bam_qc": {
                    "type": "boolean",
                    "description": "Skip alignment QC."
                },
                "skip_alfred": {
                    "type": "boolean",
                    "description": "Skip alred alignment QC."
                },
                "skip_samtools_flagstat": {
                    "type": "boolean",
                    "description": "Skip samtools alignment QC."
                },
                "skip_cramino": {
                    "type": "boolean",
                    "description": "Skip cramino alignment QC."
                },
                "cramino_min_length": {
                    "type": "integer",
                    "default": 0,
                    "description": "Minimum length of alignments considered by cramino."
                },
                "skip_ngs_bits": {
                    "type": "boolean",
                    "description": "Skip ngs bits alignment QC."
                },
                "ngs_bits_skip_contamination": {
                    "type": "boolean",
                    "description": "Skip ngs bit contamination detection."
                },
                "ngs_bits_build": {
                    "type": "string",
                    "default": "hg38",
                    "description": "Ngs bits genome build (hg38)."
                },
                "skip_mapping": {
                    "type": "boolean",
                    "description": "Skip mapping to reference genome."
                },
                "skip_bam_to_bigwig": {
                    "type": "boolean",
                    "description": "Skip creation of bigWig alignment files for viewing in genome browsers."
                },
                "skip_flair": {
                    "type": "boolean",
                    "description": "Skip FLAIR transcript reconstruction."
                },
                "skip_flair_correct": {
                    "type": "boolean",
                    "description": "Skip FLAIR correct module.",
                    "default": true
                },
                "extra_flair_correct_options": {
                    "type": "string",
                    "description": "Additional options for FLAIR correct."
                },
                "skip_flair_collapse": {
                    "type": "boolean",
                    "description": "Skip FLAIR collapse module."
                },
                "extra_flair_collapse_options": {
                    "type": "string",
                    "description": "Additional options for FLAIR collapse."
                },
                "skip_bambu": {
                    "type": "boolean",
                    "description": "Skip bambu transcript reconstruction."
                },
                "extra_bambu_options": {
                    "type": "string",
                    "description": "Additional options for bambu."
                },
                "skip_stringtie": {
                    "type": "boolean",
                    "description": "Skip StringTie transcript reconstruction."
                },
                "extra_stringtie_options": {
                    "type": "string",
                    "description": "Additional options for StringTie."
                },
                "skip_isoquant": {
                    "type": "boolean",
                    "description": "Skip IsoQuant transcript reconstruction."
                },
                "skip_isoquant_correction": {
                    "type": "boolean",
                    "description": "Skip IsoQuant read correction."
                },
                "extra_isoquant_options": {
                    "type": "string",
                    "description": "Additional options for IsoQuant."
                },
                "skip_jaccard": {
                    "type": "boolean",
                    "description": "Skip calculation of jaccard statistic."
                },
                "skip_gffcompare": {
                    "type": "boolean",
                    "description": "Skip gffcompare transcirptome assessment."
                },
                "extra_gffcompare_options": {
                    "type": "string",
                    "description": "Additional gffcompare options."
                },
                "skip_sqanti_all": {
                    "type": "boolean",
                    "description": "Skip all of SQANTI modules."
                },
                "skip_sqanti_qc": {
                    "type": "boolean",
                    "description": "Skip SQANTI QC module."
                },
                "sqanti_qc_reference": {
                    "type": "string",
                    "default": "human",
                    "description": "Reference genome name for SQANTI QC.",
                    "help_text": "Only supports 'human' currently."
                },
                "sqanti_qc_cage": {
                    "type": "boolean",
                    "default": true,
                    "description": "Use CAGE data with SQANTI QC."
                },
                "sqanti_qc_cage_path": {
                    "type": "string",
                    "description": "Path to SQANTI QC CAGE data."
                },
                "sqanti_qc_polyA_sites": {
                    "type": "boolean",
                    "default": true,
                    "description": "Use polyA sites data with SQANTI QC."
                },
                "sqanti_qc_polyA_sites_path": {
                    "type": "string",
                    "description": "Path to SQANTI QC polyA sites data."
                },
                "sqanti_qc_polyA_motif": {
                    "type": "boolean",
                    "default": true,
                    "description": "Use polyA motif data with SQANTI QC."
                },
                "sqanti_qc_polyA_motif_path": {
                    "type": "string",
                    "description": "Path to SQANTI QC polyA motif data."
                },
                "sqanti_qc_intron_junctions": {
                    "type": "boolean",
                    "default": true,
                    "description": "Use intron junction data with SQANTI QC."
                },
                "sqanti_qc_intron_path": {
                    "type": "string",
                    "description": "Path to SQANTI QC intron site data."
                },
                "extra_sqanti_qc_options": {
                    "type": "string",
                    "description": "Additional options for SQANTI QC."
                },
                "skip_jaffal": {
                    "type": "boolean",
                    "description": "Skip JAFFAL fusion gene detection.",
                    "default": true
                },
                "skip_jaffal_download": {
                    "type": "boolean",
                    "description": "Skip download of JAFFAL reference (recommended).",
                    "default": true
                },
                "jaffal_reference": {
                    "type": "string",
                    "description": "Path to JAFFAL reference directory."
                },
                "skip_transcript_quantification": {
                    "type": "boolean",
                    "description": "Skip all transcript quantification."
                },
                "skip_oarfish": {
                    "type": "boolean",
                    "description": "Skip OARFISH transcript quantification."
                },
                "sylph_database": {
                    "type": "string",
                    "default": "data/gtdb-r226-c1000-dbv1.syldb",
                    "description": "Path to sylph prebuilt database used for downloads - from https://sylph-docs.github.io/pre%E2%80%90built-databases/ ."
                },
                "skip_sylph": {
                    "type": "boolean",
                    "description": "Skip sylph profiling of unmapped reads."
                },
                "sylph_database_name": {
                    "type": "string",
                    "default": "GTDB_r226",
                    "description": "Name of sylph database, must be identical to those given in https://sylph-docs.github.io/pre%E2%80%90built-databases/ , with spaces replaced with underscores."
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/$defs/reference_genome_options"
        },
        {
            "$ref": "#/$defs/input_output_options"
        },
        {
            "$ref": "#/$defs/multiqc_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        },
        {
            "$ref": "#/$defs/module_specific_options"
        }
    ]
}