Add models for parsing quality metrics

cg/meta/workflow/microsalt/models.py

@@ -0,0 +1,41 @@
+from typing import List, Dict
+from pydantic import BaseModel
+
+
+class BlastPubmlst(BaseModel):
+    sequence_type: str
+    thresholds: str
+
+
+class QuastAssembly(BaseModel):
+    estimated_genome_length: int
+    gc_percentage: str
+    n50: int
+    necessary_contigs: int
+
+
+class PicardMarkduplicate(BaseModel):
+    insert_size: int
+    duplication_rate: float
+
+
+class MicrosaltSamtoolsStats(BaseModel):
+    total_reads: int
+    mapped_rate: float
+    average_coverage: float
+    coverage_10x: float
+    coverage_30x: float
+    coverage_50x: float
+    coverage_100x: float
+
+
+class Sample(BaseModel):
+    blast_pubmlst: BlastPubmlst
+    quast_assembly: QuastAssembly
+    blast_resfinder_resistence: List[str]
+    picard_markduplicate: PicardMarkduplicate
+    microsalt_samtools_stats: MicrosaltSamtoolsStats
+
+
+class QualityMetrics(BaseModel):
+    samples: Dict[str, Sample]