nextflow_schema.json

{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/aineniamh/squirrel/main/nextflow_schema.json",
  "title": "aineniamh/squirrel",
  "description": "Some QUIck Rearranging to Resolve Evolutionary Links.",
  "url": "https://github.com/aineniamh/squirrel",
  "type": "object",
  "definitions": {
    "input_options": {
      "title": "Input Options",
      "type": "object",
      "fa_icon": "fas fa-terminal",
      "description": "Define where the pipeline should find input data and save output data.",
      "properties": {
        "fasta": {
          "type": "string",
          "format": "file-path",
          "title": "FASTA",
          "description": "",
          "help_text": ""
        },
        "clade": {
          "type": "string",
          "title": "Clade",
          "description": "Specify whether the alignment is primarily for 'cladei' or 'cladeii'.",
          "enum": [
            "cladei",
	        "cladeia",
	        "cladeib",
            "cladeii",
            "cladeiia",
            "cladeiib"
          ],
          "help_text": ""
        },
        "seq_qc": {
          "type": "boolean",
          "default": false,
          "title": "Run Sequence QC",
          "description": "Flag potentially problematic SNPs and sequences.",
          "help_text": "Note that if 'Run Phylo' is also selected this additionally runs qc based on the phylogenetic tree."
        },
        "additional_mask": {
          "type": "string",
          "format": "path",
          "title": "Additional Mask",
          "description": "CSV file describing additional sites to mask.",
          "help_text": "Squirrel can be run twice, and the sites file generated the first time can be passed back."
        },
        "run_phylo": {
          "type": "boolean",
          "default": false,
          "title": "Run Phylo",
          "description": "Run phylogenetics pipeline",
          "help_text": ""
        },
        "run_apobec3_phylo": {
          "type": "boolean",
          "default": false,
          "title": "Run APOBEC3 Phylo",
          "description": "Run phylogenetics & APOBEC3-mutation reconstruction pipeline",
          "help_text": ""
        },
        "include_background": {
          "type": "boolean",
          "default": false,
          "title": "Include Background",
          "description": "Include a default background set of sequences for the phylogenetics pipeline. ",
          "help_text": "The set will be determined by the `--clade` specified. Only the included outgroup sequences will be used, not those specified with 'Outgroups'."
        },
        "additional_background": {
          "type": "string",
          "format": "file-path",
          "title": "Additional Background",
          "description": "Include this additional FASTA file as background to the phylogenetics",
          "help_text": ""
        },
        "outgroups": {
          "type": "string",
          "title": "Outgroups",
          "description": "Specify which MPXV outgroup(s) in the alignment to use in the phylogeny. ",
          "help_text": "These are used only by the phylogenetics module and will get pruned out from the final tree. These must be in the input FASTA. Ignored if 'Include Background' is selected."
        },
        "assembly_refs": {
          "type": "string",
          "format": "file-path",
          "title": "Assembly References",
          "description": "References to check for `calls to reference` against, used only by the sequence QC process.",
          "help_text": ""
        }
      },
      "required": [
        "fasta",
        "clade"
      ]
    },
    "output_options": {
      "title": "Output Options",
      "type": "object",
      "description": "Parameters for saving and naming workflow outputs.",
      "properties": {
        "out_dir": {
          "type": "string",
          "format": "directory-path",
          "default": "output",
          "title": "Output folder name",
          "description": "Directory for output of all user-facing files."
        }
      }
    },
    "advanced_options": {
      "title": "Advanced Options",
      "type": "object",
      "description": "Advanced options for configuring processes inside the workflow.",
      "default": "",
      "properties": {
        "no_mask": {
          "type": "boolean",
          "default": false,
          "title": "Skip mask of repetitive regions",
          "description": "",
          "help_text": ""
        },
        "no_itr_mask": {
          "type": "boolean",
          "default": false,
          "title": "Skip mask end of ITR",
          "description": "",
          "help_text": ""
        },
        "extract_cds": {
          "type": "boolean",
          "default": false,
          "title": "Extract CDS ",
          "description": "",
          "help_text": "Extract ccoding sequences based on coordinates in the reference."
        },
        "concatenate": {
          "type": "boolean",
          "default": false,
          "title": "Concatenate CDS ",
          "description": "Concatenate coding sequences for each genome, separated by `NNN`.",
          "help_text": "Default: write out as separate records."
        },
        "extra_flags": {
          "type": "string",
          "title": "Extra flags ",
          "description": "Additional command line arguments to be passed to squirrel.",
          "help_text": ""
        }
      }
    },
    "miscellaneous_options": {
      "title": "Miscellaneous Options",
      "type": "object",
      "fa_icon": "fas fa-file-import",
      "description": "Everything else.",
      "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
      "properties": {
        "help": {
          "type": "boolean",
          "title": "Display help text",
          "fa_icon": "fas fa-question-circle",
          "hidden": true
        },
        "version": {
          "type": "boolean",
          "title": "Display version",
          "description": "Display version and exit.",
          "fa_icon": "fas fa-question-circle",
          "hidden": true
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/input_options"
    },
    {
      "$ref": "#/definitions/output_options"
    },
    {
      "$ref": "#/definitions/advanced_options"
    },
    {
      "$ref": "#/definitions/miscellaneous_options"
    }
  ],
  "properties": {
    "aws_image_prefix": {
      "type": "string",
      "title": "AWS image prefix",
      "hidden": true
    },
    "aws_queue": {
      "type": "string",
      "title": "AWS queue",
      "hidden": true
    },
    "monochrome_logs": {
      "type": "boolean"
    },
    "validate_params": {
      "type": "boolean",
      "default": true
    },
    "show_hidden_params": {
      "type": "boolean"
    }
  },
  "docs": {
    "intro": "\nasquirrel is an analysis tool to run QC and alignment and to construct phylogenetic trees, developed for mpxv.\n\n",
    "links": "## Useful links\n\n* [nextflow](https://www.nextflow.io/)\n* [docker](https://www.docker.com/products/docker-desktop)"
  }
}