{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "leiden",
  "description": "Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy framework] [Wolf18]. \nLeiden is an improved version of the [Louvain algorithm] [Blondel08]. \nIt has been proposed for single-cell analysis by [Levine15] [Levine15]. \nThis requires having ran `neighbors/find_neighbors` or `neighbors/bbknn` first.\n\n[Blondel08]: Blondel et al. (2008), Fast unfolding of communities in large networks, J. Stat. Mech.  \n[Levine15]: Levine et al. (2015), Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis, Cell.  \n[Traag18]: Traag et al. (2018), From Louvain to Leiden: guaranteeing well-connected communities arXiv.  \n[Wolf18]: Wolf et al. (2018), Scanpy: large-scale single-cell gene expression data analysis, Genome Biology.  \n",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input file.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.h5mu\"`. "
        },
        "modality": {
          "type": "string",
          "description": "Which modality from the input MuData file to process.\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\"rna\"`. ",
          "default": "rna"
        },
        "obsp_connectivities": {
          "type": "string",
          "description": "In which .obsp slot the neighbor connectivities can be found.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"connectivities\"`. ",
          "default": "connectivities"
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output file.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        },
        "obsm_name": {
          "type": "string",
          "description": "Name of the .obsm key under which to add the cluster labels.\nThe name of the columns in the matrix will correspond to the resolutions.\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\"leiden\"`. ",
          "default": "leiden"
        },
        "resolution": {
          "type": "array",
          "items": {
            "type": "number"
          },
          "description": "A parameter value controlling the coarseness of the clustering",
          "help_text": "Type: `double`, multiple: `True`, required, default: `[1.0]`. ",
          "default": [
            1.0
          ]
        },
        "output_compression": {
          "type": "string",
          "description": "Compression format to use for the output AnnData and/or Mudata objects.\nBy default no compression is applied.\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"gzip\"`, choices: ``gzip`, `lzf``. ",
          "enum": [
            "gzip",
            "lzf"
          ]
        }
      }
    },
    "nextflow input-output arguments": {
      "title": "Nextflow input-output arguments",
      "type": "object",
      "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
      "properties": {
        "publish_dir": {
          "type": "string",
          "description": "Path to an output directory.",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/$defs/arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
