diff --git a/schemas/qc_metrics.json b/schemas/qc_metrics.json index dbc8908..e8ab2bb 100644 --- a/schemas/qc_metrics.json +++ b/schemas/qc_metrics.json @@ -13,7 +13,6 @@ "workflow_name", "workflow_short_name", "workflow_version", - "analysis_tools", "genome_build", "run_id", "inputs" @@ -22,7 +21,6 @@ "required": [ "workflow_name", "workflow_version", - "analysis_tools", "genome_build", "run_id", "inputs" @@ -33,14 +31,11 @@ "properties": { "workflow_name": { "type": "string", - "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$" + "pattern": "^[a-zA-Z][a-zA-Z0-9 _\\-]+[a-zA-Z0-9]+$" }, "workflow_short_name": { "type": "string", - "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$" - }, - "analysis_tools": { - "const": null + "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+[a-zA-Z0-9]+$" }, "genome_build": { "type": "string", diff --git a/schemas/sequencing_alignment.json b/schemas/sequencing_alignment.json index 176ff47..a92f445 100644 --- a/schemas/sequencing_alignment.json +++ b/schemas/sequencing_alignment.json @@ -14,7 +14,6 @@ "enum": [ "workflow_name", "workflow_version", - "analysis_tools", "genome_build", "run_id", "inputs" @@ -23,7 +22,6 @@ "required": [ "workflow_name", "workflow_version", - "analysis_tools", "genome_build", "run_id", "inputs" @@ -34,14 +32,7 @@ "properties": { "workflow_name": { "type": "string", - "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$" - }, - "analysis_tools": { - "type": ["array", "null"], - "items": { - "type": "string", - "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$" - } + "pattern": "^[a-zA-Z][a-zA-Z0-9 _\\-]+[a-zA-Z0-9]+$" }, "genome_build": { "type": "string", diff --git a/schemas/variant_calling.json b/schemas/variant_calling.json index d94fe52..d0e9399 100644 --- a/schemas/variant_calling.json +++ b/schemas/variant_calling.json @@ -5,8 +5,7 @@ "required": [ "workflow", "experiment", - "variant_class", - "variant_type" + "variant_class" ], "properties": { "workflow": { @@ -15,7 +14,6 @@ "workflow_name", "workflow_short_name", "workflow_version", - "analysis_tools", "genome_build", "run_id", "inputs" @@ -25,7 +23,6 @@ "workflow_name", "workflow_short_name", "workflow_version", - "analysis_tools", "genome_build", "run_id", "inputs" @@ -34,18 +31,11 @@ "properties": { "workflow_name": { "type": "string", - "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$" + "pattern": "^[a-zA-Z][a-zA-Z0-9 _\\-]+[a-zA-Z0-9]+$" }, "workflow_short_name": { "type": "string", - "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$" - }, - "analysis_tools": { - "type": ["array", "null"], - "items": { - "type": "string", - "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$" - } + "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+[a-zA-Z0-9]+$" }, "genome_build": { "type": "string", @@ -121,26 +111,11 @@ } }, "variant_class": { - "type": "array", - "items":{ - "type": "string", - "enum": [ - "germline", - "somatic" - ] - } - }, - "variant_type": { - "type": "array", - "items":{ - "type": "string", - "enum": [ - "snv", - "indel", - "cnv", - "sv" - ] - } + "type": "string", + "enum": [ + "Germline", + "Somatic" + ] } } } diff --git a/schemas/variant_calling_supplement.json b/schemas/variant_calling_supplement.json index 2be194c..76818cb 100644 --- a/schemas/variant_calling_supplement.json +++ b/schemas/variant_calling_supplement.json @@ -4,7 +4,8 @@ "type": "object", "required": [ "workflow", - "experiment" + "experiment", + "variant_class" ], "properties": { "workflow": { @@ -13,7 +14,6 @@ "workflow_name", "workflow_short_name", "workflow_version", - "analysis_tools", "genome_build", "run_id", "inputs" @@ -23,7 +23,6 @@ "workflow_name", "workflow_short_name", "workflow_version", - "analysis_tools", "genome_build", "run_id", "inputs" @@ -32,14 +31,11 @@ "properties": { "workflow_name": { "type": "string", - "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$" + "pattern": "^[a-zA-Z][a-zA-Z0-9 _\\-]+[a-zA-Z0-9]+$" }, "workflow_short_name": { "type": "string", - "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$" - }, - "analysis_tools": { - "const": null + "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+[a-zA-Z0-9]+$" }, "genome_build": { "type": "string", @@ -111,6 +107,13 @@ "Bisulfite-Seq", "ChIP-Seq" ] + }, + "variant_class": { + "type": "string", + "enum": [ + "Germline", + "Somatic" + ] } } }