{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "from_cellranger_multi_to_h5mu",
  "description": "Converts the output from cellranger multi to a single .h5mu file.\nBy default, will map the following library type names to modality names:\n  - Gene Expression: rna\n  - Peaks: atac\n  - Antibody Capture: prot\n  - VDJ: vdj\n  - VDJ-T: vdj_t\n  - VDJ-B: vdj_b\n  - CRISPR Guide Capture: crispr\n  - Multiplexing Capture: hashing\n  \nOther library types have their whitepace removed and dashes replaced by\nunderscores to generate the modality name.\n\nCurrently does not allow parsing the output from cell barcode demultiplexing.\n",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input folder",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input_dir_containing_modalities\"`. "
        },
        "output": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "description": "Locations for the output files",
          "help_text": "Type: `file`, multiple: `True`, default: `\"$id.$key.output_*.h5mu\"`, direction: `output`, example: `[\"*.h5mu\"]`. ",
          "default": "$id.$key.output_*.h5mu"
        },
        "sample_csv": {
          "type": "string",
          "format": "path",
          "description": "CSV file describing the sample name per output file",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.sample_csv.csv\"`, direction: `output`, example: `\"samples.csv\"`. ",
          "default": "$id.$key.sample_csv.csv"
        },
        "uns_metrics": {
          "type": "string",
          "description": "Name of the .uns slot under which to QC metrics (if any).",
          "help_text": "Type: `string`, multiple: `False`, default: `\"metrics_cellranger\"`. ",
          "default": "metrics_cellranger"
        },
        "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"
    }
  ]
}
