nextflow_schema.json

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "documents": {
      "type": "object",
      "additionalProperties": {
        "type": "object",
        "properties": {
          "skyline": {
            "type": "string"
          },
          "metadata": {
            "type": "string"
          }
        },
        "required": ["skyline"]
      },
      "description": "A map of Skyline documents and metadata files; file paths can be local file paths or Panorama WebDav URLs"
    },
    "result_dir": {
      "type": "string",
      "default": "results/dia_batch_correction",
      "description": "Directory to write result files."
    },
    "report_dir": {
      "type": "string",
      "default": "reports/dia_batch_correction",
      "description": "Directory to write report files."
    },
    "skyline": {
      "type": "object",
      "properties": {
        "group_by_gene": {
          "type": "boolean",
          "default": false,
          "description": "Group data by gene in Skyline."
        }
      }
    },
    "precursor_report_template": {
      "type": "string",
      "default": "https://raw.githubusercontent.com/uw-maccosslab/nf-dia-batch-correction/master/resources/precursor_quality.skyr",
      "description": "URL template for precursor quality report.",
      "hidden": true
    },
    "replicate_report_template": {
      "type": "string",
      "default": "https://raw.githubusercontent.com/uw-maccosslab/nf-dia-batch-correction/master/resources/replicate_quality.skyr",
      "description": "URL template for replicate quality report.",
      "hidden": true
    },
    "panorama": {
      "type": "object",
      "properties": {
        "domain": {
          "type": "string",
          "default": "https://panoramaweb.org",
          "description": "Panorama domain."
        },
        "skyline_folder": {
          "type": ["string", "null"],
          "default": null,
          "description": "Panorama Skyline folder."
        },
        "reports_folder": {
          "type": ["string", "null"],
          "default": null,
          "description": "Panorama reports folder."
        }
      }
    },
    "normalize_db": {
      "type": "object",
      "properties": {
        "exclude_replicates": {
          "type": ["array", "null"],
          "items": {
            "type": "string"
          },
          "default": null,
          "description": "List of replicates to exclude from normalization and batch correction"
        },
        "exclude_projects": {
          "type": ["array", "null"],
          "items": {
            "type": "string"
          },
          "default": null,
          "description": "List of Skyline documents to exclude from normalization and batch correction"
        },
        "method": {
          "type": "string",
          "enum": ["DirectLFQ", "median"],
          "default": "DirectLFQ",
          "description": "Normalization method to use. Options are 'DirectLFQ' and 'median'"
        }
      }
    },
    "impute": {
      "type": "object",
      "properties": {
        "method": {
          "type": "string",
          "enum" : ["knn"],
          "description": "Method to use for imputation of missing precursor quantities. Choose from 'knn'."
        }
      }
    },
    "bc": {
      "type": "object",
      "properties": {
        "method": {
          "type": "string",
          "default": "combat",
          "description": "Batch correction method"
        },
        "batch1": {
          "type": ["string", "null"],
          "default": null,
          "description": "Metadata key corresponding to batch level 1. If null, the project name is used as the batch variable"
        },
        "batch2": {
          "type": ["string", "null"],
          "default": null,
          "description": "Metadata key corresponding to batch level 2. If null, the project name is used as the batch variable"
        },
        "color_vars": {
          "type": ["string", "array", "null"],
          "items": {
            "type": "string"
          },
          "default": null,
          "description": "Metadata key(s) used to color PCA plots. Can be either string or list. If null, batch and acquisition number are used to color plots."
        },
        "covariate_vars": {
          "type": ["string", "array", "null"],
          "items": {
            "type": "string"
          },
          "default": null,
          "description": "Metadata key(s) to use as covariates for batch correction. Can be either string or list. If null, no covariates are used."
        },
        "control_key": {
          "type": ["string", "null"],
          "default": null,
          "description": "Metadata key indicating replicates which are controls for CV plots. If null, all replicates are used in CV distribution plot."
        },
        "control_values": {
          "type": ["array", "null"],
          "items": {
            "type": "string"
          },
          "default": null,
          "description": "Metadata value(s) mapping to control_key indicating whether a replicate is a control."
        },
        "plot_ext": {
          "type": ["string", "null"],
          "default": null,
          "description": "File extension for standalone plots. If null, no standalone plots are produced."
        }
      }
    },
    "aws": {
      "type": "object",
      "properties": {
        "region": {
          "type": "string",
          "default": "us-west-2"
        },
        "batch": {
          "type": "object",
          "properties": {
            "cliPath": {
              "type": "string",
              "default": "/usr/local/aws-cli/v2/current/bin/aws"
            },
            "logsGroup": {
              "type": "string",
              "default": "/batch/tei-nextflow-batch"
            },
            "maxConnections": {
              "type": "integer",
              "default": 20
            },
            "connectionTimeout": {
              "type": "integer",
              "default": 10000
            },
            "uploadStorageClass": {
              "type": "string",
              "default": "INTELLIGENT_TIERING"
            },
            "storageEncryption": {
              "type": "string",
              "default": "AES256"
            },
            "retryMode": {
              "type": "string",
              "default": "standard"
            }
          }
        }
      }
    },
    "max_memory": {
      "type": "string",
      "default": "12.GB"
    },
    "max_cpus": {
      "type": "integer",
      "default": 8
    },
    "max_time": {
      "type": "string",
      "default": "240.h"
    },
    "images": {
      "type": "object",
      "properties": {
        "linux": {
          "type": "string",
          "default": "quay.io/mauraisa/aws_bash:latest"
        },
        "panorama_client": {
          "type": "string",
          "default": "quay.io/protio/panorama-client:1.1.0"
        },
        "proteowizard": {
          "type": "string",
          "default": "quay.io/mauraisa/pwiz-skyline-i-agree-to-the-vendor-licenses:skyline_daily_25.0.9.97-ae4c997"
        },
        "batch_report": {
          "type": "string",
          "default": "quay.io/mauraisa/dia_qc_report:2.5.0"
        }
      },
      "additionalProperties": false,
      "hidden": true
    }
  }
}