{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "calculate_atac_qc_metrics",
  "description": "Add basic ATAC quality control metrics to an .h5mu file.\n\nThe metrics are comparable to what scanpy.pp.calculate_qc_metrics output,\nalthough they have slightly different names:\n\nObs metrics (name in this component -> name in scanpy):\n  - n_features_per_cell -> n_genes_by_counts\n  - total_fragment_counts -> total_counts\n    \n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input h5mu file",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.h5mu\"`. "
        },
        "fragments_path": {
          "type": "string",
          "format": "path",
          "description": "Path to the fragments file",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"fragments.tsv.gz\"`. "
        },
        "modality": {
          "type": "string",
          "description": "Which modality from the input MuData file to process.\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\"atac\"`. ",
          "default": "atac"
        },
        "layer": {
          "type": "string",
          "description": "Layer at `.layers` to use for the calculation",
          "help_text": "Type: `string`, multiple: `False`, example: `\"raw_counts\"`. "
        },
        "n_fragments_for_nucleosome_signal": {
          "type": "integer",
          "description": "Number of fragments to use per cell for nucleosome signal calculation.\nTakes very long to calculate, for a test run lower value (e.g",
          "help_text": "Type: `integer`, multiple: `False`, default: `100000`. ",
          "default": 100000
        },
        "nuc_signal_threshold": {
          "type": "number",
          "description": "Threshold for nucleosome signal",
          "help_text": "Type: `double`, multiple: `False`, default: `2.0`. ",
          "default": 2.0
        },
        "n_tss": {
          "type": "integer",
          "description": "Number of the transcription start sites to calculate TSS enrichment score.\nSee https://www.sc-best-practices.org/chromatin_accessibility/quality_control.html#tss-enrichment\nfor more information\n",
          "help_text": "Type: `integer`, multiple: `False`, default: `3000`. ",
          "default": 3000
        },
        "tss_threshold": {
          "type": "number",
          "description": "Threshold for TSS enrichment score",
          "help_text": "Type: `double`, multiple: `False`, default: `1.5`. ",
          "default": 1.5
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output h5mu file.",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        },
        "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/inputs"
    },
    {
      "$ref": "#/$defs/outputs"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
