diff --git a/config.yaml b/config.yaml
new file mode 100644
index 0000000..3563fb1
--- /dev/null
+++ b/config.yaml
@@ -0,0 +1,12 @@
+metrics_output_tsv:
+  dragen_2.6.2.4: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
+  localapp_ruo-2.2.0.12: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
+small_variant_genome_vcf:
+  dragen_2.6.2.4: Logs_Intermediates/DnaDragenCaller/{}/{}.hard-filtered.gvcf.gz
+  localapp_ruo-2.2.0.12: Logs_Intermediates/VariantMatching/{}/{}_MergedSmallVariants.genome.vcf
+tmb_trace_tsv:
+  dragen_2.6.2.4: Logs_Intermediates/Tmb/{}/{}.tmb.trace.tsv
+  localapp_ruo-2.2.0.12: Logs_Intermediates/Tmb/{}/{}_TMB_Trace.tsv
+variants_annotated_json:
+  dragen_2.6.2.4: Logs_Intermediates/Annotation/{}/{}_DNAVariants_Annotated.json
+  localapp_ruo-2.2.0.12: Logs_Intermediates/Annotation/{}/{}_SmallVariants_Annotated.json.gz
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index d284de1..78cfce8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,6 +7,7 @@ dependencies = [
     "cyvcf2>=0.32.1",
     "msgspec>=0.21.1",
     "polars>=1.39.3",
+    "pyyaml>=6.0.3",
     "typer>=0.24.1",
 ]
 dynamic = ["version"]
diff --git a/src/tsoppy/general/classes.py b/src/tsoppy/general/classes.py
new file mode 100644
index 0000000..d1f60bd
--- /dev/null
+++ b/src/tsoppy/general/classes.py
@@ -0,0 +1,207 @@
+import logging
+import os
+from pathlib import Path
+
+import cyvcf2
+import msgspec
+import polars
+
+from tsoppy.general.file_parser import Parse_section_tsv
+
+# Use logger that was set up in CLI
+logger = logging.getLogger(__name__)
+
+
+class WorkflowConfig(msgspec.Struct):
+    """Config class for workflow output file path format strings"""
+
+    metrics_output_tsv: dict[str, str]
+    small_variant_genome_vcf: dict[str, str]
+    tmb_trace_tsv: dict[str, str]
+    variants_annotated_json: dict[str, str]
+
+    def __eq__(self, other):
+        if not isinstance(other, WorkflowConfig):
+            return False
+        if self.metrics_output_tsv != other.metrics_output_tsv:
+            return False
+        if self.small_variant_genome_vcf != other.small_variant_genome_vcf:
+            return False
+        if self.tmb_trace_tsv != other.tmb_trace_tsv:
+            return False
+        return self.variants_annotated_json == other.variants_annotated_json
+
+
+class WorkflowOutput:
+    """Base class for outputs produced by different workflows (e.g. dragen/localapp).
+
+    Attributes:
+        config: Configuration (WorkflowConfig)
+        root: Root path (Path)
+        workflow_type: Detected workflow type (str)
+        workflow_version: Detected workflow version (str)
+    """
+
+    def __init__(self, config_yaml: str | Path, root_path: str | Path):
+        """Initialize WorkflowOutput."""
+        self.root = Path(root_path)
+        with open(config_yaml, "r") as yaml_file:
+            self.config = msgspec.yaml.decode(yaml_file.read(), type=WorkflowConfig)
+
+        self._detect_type_and_version()
+
+    def _detect_type_and_version(self):
+        """Detect which workflow type and version is present based on information in MetricsOutput.tsv."""
+
+        # Get all values for MetricsOutput.tsv paths and check if they are the same
+        info_src = list(self.config.metrics_output_tsv.values())
+        if len(set(info_src)) != 1:
+            raise ValueError(
+                f"Got {info_src} but need exactly one file to detect workflow id"
+            )
+
+        # Parse MetricsOutput.tsv
+        headers, sections = Parse_section_tsv(
+            os.path.join(self.root, info_src[0]), ["Header"]
+        )
+
+        # Check if DRAGEN is part of the header and assume the data is localapp if not
+        if "DRAGEN" in headers[0]:
+            self.workflow_type = "dragen"
+        else:
+            self.workflow_type = "localapp"
+
+        # Set workflow version from Header section
+        self.workflow_version = sections["Header"].item(
+            row=0, column="Workflow Version"
+        )
+
+    def __eq__(self, other):
+        if not isinstance(other, WorkflowOutput):
+            return False
+        if self.config != other.config:
+            return False
+        if self.root != other.root:
+            return False
+        if self.workflow_type != other.workflow_type:
+            return False
+        return self.workflow_version == other.workflow_version
+
+    def workflow_id(self):
+        """Return combined string for workflow type and version."""
+        return f"{self.workflow_type}_{self.workflow_version}"
+
+
+class SmallVariantGenomeVcf(WorkflowOutput):
+    """Input class for small variant genome VCF files produced by different workflows.
+
+    Attributes:
+        path: Path to vcf (Path)
+        sample_id: Sample identifier (str)
+        vcf: Parsed VCF object (cyvcf2.VCF)
+    """
+
+    def __init__(self, config_yaml: str | Path, root_path: str | Path, sample_id: str):
+        """Initialize SmallVariantGenomeVcf"""
+        super().__init__(config_yaml, root_path)
+        self.sample_id = sample_id
+        self._parse()
+
+    @classmethod
+    def create(cls, workflow_output: WorkflowOutput, sample_id: str):
+        """Create SmallVariantGenomeVcf from existing WorkflowOutput"""
+        obj = cls.__new__(cls)
+        obj.__dict__.update(workflow_output.__dict__)
+        obj.sample_id = sample_id
+        obj._parse()
+        return obj
+
+    def _parse(self):
+        """Parse the small variant genome VCF file"""
+        fmt = self.config.small_variant_genome_vcf[self.workflow_id()]
+        self.path = Path(
+            os.path.join(self.root, fmt.format(self.sample_id, self.sample_id))
+        )
+        if not self.path.is_file():
+            logging.error(
+                f"Small variant genome VCF missing: File {self.path} does not exist."
+            )
+            raise FileNotFoundError
+        self.vcf = cyvcf2.VCF(self.path)
+
+
+class TmbTraceTsv(WorkflowOutput):
+    """Input class for TMB trace files produced by different workflows.
+
+    Attributes:
+        path: Path to vcf (Path)
+        rows: Parsed rows of the TMB trace file (polars.DataFrame)
+        sample_id: Sample identifier (str)
+    """
+
+    def __init__(self, config_yaml: str | Path, root_path: str | Path, sample_id: str):
+        """Initialize TmTraceTsv."""
+        super().__init__(config_yaml, root_path)
+        self.sample_id = sample_id
+        self._parse()
+
+    @classmethod
+    def create(cls, workflow_output: WorkflowOutput, sample_id: str):
+        """Create TmbTraceTsv from existing WorkflowOutput."""
+        obj = cls.__new__(cls)
+        obj.__dict__.update(workflow_output.__dict__)
+        obj.sample_id = sample_id
+        obj._parse()
+        return obj
+
+    def _parse(self):
+        """Parse the TMB trace tsv."""
+        fmt = self.config.tmb_trace_tsv[self.workflow_id()]
+        self.path = Path(
+            os.path.join(self.root, fmt.format(self.sample_id, self.sample_id))
+        )
+        if not self.path.is_file():
+            logging.error(
+                f"Small variant genome VCF missing: File {self.path} does not exist."
+            )
+            raise FileNotFoundError
+        self.table = polars.read_csv(self.path, separator="\t")
+
+
+class VariantsAnnotatedJson(WorkflowOutput):
+    """Input class for annotated JSON files produced by different workflows.
+
+    Attributes:
+        path: Path to vcf (Path)
+        data: Parsed JSON data (dict)
+        sample_id: Sample identifier (str)
+    """
+
+    def __init__(self, config_yaml: str | Path, root_path: str | Path, sample_id: str):
+        """Initialize VariantsAnnotatedJson."""
+        super().__init__(config_yaml, root_path)
+        self.sample_id = sample_id
+        self._parse()
+
+    @classmethod
+    def create(cls, workflow_output: WorkflowOutput, sample_id: str):
+        """Create VariantsAnnotatedJson from existing WorkflowOutput."""
+        obj = cls.__new__(cls)
+        obj.__dict__.update(workflow_output.__dict__)
+        obj.sample_id = sample_id
+        obj._parse()
+        return obj
+
+    def _parse(self):
+        """Parse the variants annotated JSON file"""
+        fmt = self.config.variants_annotated_json[self.workflow_id()]
+        self.path = Path(
+            os.path.join(self.root, fmt.format(self.sample_id, self.sample_id))
+        )
+        if not self.path.is_file():
+            logging.error(
+                f"Small variant genome VCF missing: File {self.path} does not exist."
+            )
+            raise FileNotFoundError
+        with open(self.path, "r") as file:
+            self.data = msgspec.json.decode(file.read())
diff --git a/tests/general_classes_test.py b/tests/general_classes_test.py
new file mode 100644
index 0000000..4bf9f84
--- /dev/null
+++ b/tests/general_classes_test.py
@@ -0,0 +1,46 @@
+from os import path
+from contextlib import nullcontext
+from pytest import mark, raises
+
+from tsoppy.general.classes import (
+    WorkflowOutput,
+    SmallVariantGenomeVcf
+)
+
+# Define path to test data - cannot be absolute due to different paths locally and in CI
+test_data_dir = "tests/test_data/general_classes"
+
+
+@mark.parametrize(
+    "inputs, exception, want",
+    [
+        (
+            (
+                'config.yaml',
+                path.join(test_data_dir, "dragen/standard")
+            ),
+            nullcontext(),
+            'dragen_2.6.2.4'
+        ),
+        (
+            (
+                'config.yaml',
+                path.join(test_data_dir, "localapp/standard")
+            ),
+            nullcontext(),
+            'localapp_ruo-2.2.0.12'
+        ),
+        (
+            (
+                'config.yaml',
+                path.join(test_data_dir, "localapp/non-existent")
+            ),
+            raises(FileNotFoundError),
+            ''
+        )
+    ]
+)
+def test_workflowoutput_init(inputs, exception, want):
+    with exception:
+        got = WorkflowOutput(inputs[0], inputs[1])
+        assert got.workflow_id() == want
diff --git a/tests/general_file_parser_test.py b/tests/general_file_parser_test.py
index 354115f..500d66e 100644
--- a/tests/general_file_parser_test.py
+++ b/tests/general_file_parser_test.py
@@ -12,7 +12,7 @@
 )
 
 # Define path to test data - cannot be absolute due to different paths locally and in CI
-test_data_dir = "tests/test_data/general"
+test_data_dir = "tests/test_data/general_file_parser"
 
 
 @mark.parametrize(
diff --git a/tests/test_data/general_classes/dragen/standard/Logs_Intermediates/MetricsOutput/MetricsOutput.tsv b/tests/test_data/general_classes/dragen/standard/Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
new file mode 100644
index 0000000..13f0c81
--- /dev/null
+++ b/tests/test_data/general_classes/dragen/standard/Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
@@ -0,0 +1,7 @@
+DRAGEN TruSight Oncology 500 v2.6.2 Analysis Software - Metrics Output
+For Research Use Only. Not for use in diagnostic procedures.
+
+[Header]
+Output Date	2020-01-01
+Output Time	01:00:00
+Workflow Version	2.6.2.4
\ No newline at end of file
diff --git a/tests/test_data/general_classes/localapp/standard/Logs_Intermediates/MetricsOutput/MetricsOutput.tsv b/tests/test_data/general_classes/localapp/standard/Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
new file mode 100644
index 0000000..a36c937
--- /dev/null
+++ b/tests/test_data/general_classes/localapp/standard/Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
@@ -0,0 +1,7 @@
+TruSight Oncology 500 - Metrics Output
+For Research Use Only. Not for use in diagnostic procedures.
+
+[Header]
+Output Date	2020-01-01
+Output Time	01:00:00
+Workflow Version	ruo-2.2.0.12
\ No newline at end of file
diff --git a/tests/test_data/general/parse_section_tsv/empty.tsv b/tests/test_data/general_file_parser/parse_section_tsv/empty.tsv
similarity index 100%
rename from tests/test_data/general/parse_section_tsv/empty.tsv
rename to tests/test_data/general_file_parser/parse_section_tsv/empty.tsv
diff --git a/tests/test_data/general/parse_section_tsv/empty_first_column_name.tsv b/tests/test_data/general_file_parser/parse_section_tsv/empty_first_column_name.tsv
similarity index 100%
rename from tests/test_data/general/parse_section_tsv/empty_first_column_name.tsv
rename to tests/test_data/general_file_parser/parse_section_tsv/empty_first_column_name.tsv
diff --git a/tests/test_data/general/parse_section_tsv/extra_empty_lines.tsv b/tests/test_data/general_file_parser/parse_section_tsv/extra_empty_lines.tsv
similarity index 100%
rename from tests/test_data/general/parse_section_tsv/extra_empty_lines.tsv
rename to tests/test_data/general_file_parser/parse_section_tsv/extra_empty_lines.tsv
diff --git a/tests/test_data/general/parse_section_tsv/key_value.tsv b/tests/test_data/general_file_parser/parse_section_tsv/key_value.tsv
similarity index 100%
rename from tests/test_data/general/parse_section_tsv/key_value.tsv
rename to tests/test_data/general_file_parser/parse_section_tsv/key_value.tsv
diff --git a/tests/test_data/general/parse_section_tsv/multiple_sections.tsv b/tests/test_data/general_file_parser/parse_section_tsv/multiple_sections.tsv
similarity index 100%
rename from tests/test_data/general/parse_section_tsv/multiple_sections.tsv
rename to tests/test_data/general_file_parser/parse_section_tsv/multiple_sections.tsv
diff --git a/tests/test_data/general/parse_section_tsv/no_headers.tsv b/tests/test_data/general_file_parser/parse_section_tsv/no_headers.tsv
similarity index 100%
rename from tests/test_data/general/parse_section_tsv/no_headers.tsv
rename to tests/test_data/general_file_parser/parse_section_tsv/no_headers.tsv
diff --git a/tests/test_data/general/parse_section_tsv/null_columns.tsv b/tests/test_data/general_file_parser/parse_section_tsv/null_columns.tsv
similarity index 100%
rename from tests/test_data/general/parse_section_tsv/null_columns.tsv
rename to tests/test_data/general_file_parser/parse_section_tsv/null_columns.tsv
diff --git a/tests/test_data/general/parse_section_tsv/standard.tsv b/tests/test_data/general_file_parser/parse_section_tsv/standard.tsv
similarity index 100%
rename from tests/test_data/general/parse_section_tsv/standard.tsv
rename to tests/test_data/general_file_parser/parse_section_tsv/standard.tsv