add local schema

data/api.json

+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "IGS4EU trigger pgsc_calc",
+  "type": "object",
+  "properties": {
+    "pipeline_param": {
+      "type": "object",
+      "properties": {
+        "nxf_params_file": {
+          "$ref": "nxf_params.json"
+        },
+        "target_genomes": {
+          "$ref": "samplesheet.json"
+        },
+        "nxf_work": {
+          "type": "string",
+          "description": "A path to the nextflow working directory in the ReadWriteMany Persistent Volume Claim shared by the driver and worker pods. Must be a unique path in the PVC not shared by other workflow instances, or weird things will happen."
+        },
+        "id": {
+          "type": "string",
+          "description": "An identifier assigned to the launched workflow instance. It should be universally unique to monitor the status of the launched workflow."
+        }
+      },
+      "required": [
+        "target_genomes",
+        "nxf_params_file",
+        "nxf_work",
+        "id"
+      ]
+    },
+    "globus_details": {
+      "type": "object",
+      "properties": {
+        "dir_path_on_guest_collection": {
+          "type": "string",
+          "description": "A globus endpoint ID. Files are transferred from this destination to local storage."
+        },
+        "guest_collection_id": {
+          "type": "string",
+          "description": "A globus collection ID",
+          "format": "uuid"
+        }
+      },
+        "required": [
+          "dir_path_on_guest_collection",
+          "guest_collection_id"
+        ]
+    }
+  },
+  "required": [
+    "pipeline_param",
+    "globus_details"
+  ]
+}
+

data/nxf_params.json

+{
+  "$schema": "http://json-schema.org/draft-07/schema",
+  "$id": "https://raw.githubusercontent.com/pgscatalog/pgsc_calc/dev/assets/schemas/nxf_params.json",
+  "title": "Nextflow JSON parameters for pgsc_calc",
+  "type": "object",
+  "properties": {
+    "scorefile": {
+      "type": "string",
+      "description": "Path to a scoring file"
+    },
+    "pgs_id": {
+      "type": "string",
+      "description": "PGS Catalog score ID(s), if a list separate with commas",
+      "pattern": "(PGS[0-9]{6}[,]?)+"
+    },
+    "pgp_id": {
+      "type": "string",
+      "description": "PGS Catalog publication ID(s), if a list separate with commas",
+      "pattern": "(PGP[0-9]{6}[,]?)+"
+    },
+    "trait_efo": {
+      "type": "string",
+      "description": "PGS Catalog trait ID(s), if a list separate with commas"
+    },
+    "min_overlap": {
+      "type": "number",
+      "exclusiveMinimum": 0,
+      "maximum": 1,
+      "description": "Minimum proportion of variants in target genomic data matched in the provided scorefile"
+    },
+    "max_memory": {
+      "type": "string",
+      "description": "The maximum memory used by a workflow process (worker pod limit). String uses nextflow format e.g. '4.GB'"
+    },
+    "max_cpus": {
+      "type": "integer",
+      "description": "The maximum number of CPUs used by workflow process (worker pod limit).",
+      "minimum": 1
+    },
+    "outdir": {
+      "type": "string",
+      "description": "Path to an output directory"
+    },
+    "target_build": {
+      "type": "string",
+      "enum": [
+        "GRCh37",
+        "GRCh38"
+      ],
+      "description": "Genome build of target (i.e. input) genomes"
+    }
+  },
+  "required": [
+    "target_build"
+  ],
+  "oneOf": [
+    {
+      "required": [
+        "scorefile"
+      ]
+    },
+    {
+      "required": [
+        "pgs_id"
+      ]
+    },
+    {
+      "required": [
+        "pgp_id"
+      ]
+    },
+    {
+      "required": [
+        "trait_efo"
+      ]
+    }
+  ]
+}
\ No newline at end of file

data/samplesheet.json

+{
+  "$schema": "http://json-schema.org/draft-07/schema",
+  "$id": "https://raw.githubusercontent.com/pgscatalog/pgsc_calc/dev/assets/schemas/samplesheet.json",
+  "title": "Target genome schema",
+  "description": "Validates the JSON representation of a samplesheet",
+  "type": "array",
+  "uniqueItems": true,
+  "minItems": 1,
+  "items": {
+    "type": "object",
+    "properties": {
+      "sampleset": {
+        "type": "string",
+        "pattern": "^\\S+$",
+        "description": "Sampleset name must be provided and cannot contain spaces"
+      },
+      "vcf_path": {
+        "type": [
+          "string",
+          "null"
+        ],
+        "pattern": "^\\S+\\.vcf\\.gz$",
+        "description": "VCF path must end with .vcf.gz, mutually exclusive with other formats",
+        "type": [
+          "null",
+          "string"
+        ],
+        "pattern": "^\\S+\\.vcf\\.gz$",
+        "minLength": 5
+      },
+      "vcf_genotype_field": {
+        "description": "Specify whether to import genotypes (default: GT), or imputed dosages (DS) from the VCF file.",
+        "type": [
+          "string",
+          "null"
+        ],
+        "pattern": "/^(GT|DS)$/"
+      },
+      "bed": {
+        "description": "Plink 1 binary genotype file",
+        "type": [
+          "string",
+          "null"
+        ],
+        "pattern": "^.*bed$",
+        "minLength": 5
+      },
+      "bim": {
+        "description": "Plink 1 variant information file",
+        "type": [
+          "string",
+          "null"
+        ],
+        "pattern": "^.*bim$",
+        "minLength": 5
+      },
+      "fam": {
+        "description": "Plink 1 sample information file",
+        "type": [
+          "string",
+          "null"
+        ],
+        "pattern": "^.*fam$",
+        "minLength": 5
+      },
+      "pgen": {
+        "description": "Plink 2 binary genotype file",
+        "type": [
+          "string",
+          "null"
+        ],
+        "pattern": "^.*pgen$",
+        "minLength": 6
+      },
+      "psam": {
+        "description": "Plink 2 sample information file",
+        "type": [
+          "string",
+          "null"
+        ],
+        "pattern": "^.*psam$",
+        "minLength": 6
+      },
+      "pvar": {
+        "description": "Plink 2 variant information file",
+        "type": [
+          "string",
+          "null"
+        ],
+        "pattern": "^.*pvar$",
+        "minLength": 6
+      },
+      "chrom": {
+        "description": "Specify the chromosome of associated genotyping data (must be in {1-22, X, XY, Y}). If all chromosomes are in the associated file (e.g. your data is not split by chromosome), set to null.",
+        "type": [
+          "null",
+          "string"
+        ],
+        "minLength": 1
+      }
+    },
+    "required": [
+      "sampleset",
+      "chrom"
+    ],
+    "dependentRequired": {
+      "pgen": [
+        "pvar",
+        "psam"
+      ],
+      "pvar": [
+        "pgen",
+        "psam"
+      ],
+      "psam": [
+        "pvar",
+        "pgen"
+      ],
+      "bed": [
+        "bim",
+        "fam"
+      ],
+      "bim": [
+        "fam",
+        "bed"
+      ]
+    }
+  }
+}
\ No newline at end of file