diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 09aa2de..46d590b 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -24,10 +24,10 @@ jobs:
       OS: ubuntu
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: set up python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
 
diff --git a/examples/data/string.tsv b/examples/data/string.tsv
index b007bdf..f05e8f6 100644
--- a/examples/data/string.tsv
+++ b/examples/data/string.tsv
@@ -2,9 +2,4 @@ protein1 protein2 neighborhood fusion cooccurence coexpression experimental data
 10090.ENSMUSP00000000001 10090.ENSMUSP00000020316 0 0 0 116 90 0 67 183
 10090.ENSMUSP00000000001 10090.ENSMUSP00000022816 0 0 0 62 0 0 137 155
 10090.ENSMUSP00000000001 10090.ENSMUSP00000048234 0 0 0 0 147 0 166 258
-10090.ENSMUSP00000000001 10090.ENSMUSP00000017365 0 0 0 0 165 0 0 165
-10090.ENSMUSP00000000001 10090.ENSMUSP00000033545 0 0 0 0 179 0 57 192
-10090.ENSMUSP00000000001 10090.ENSMUSP00000113105 0 0 0 0 179 0 417 500
-10090.ENSMUSP00000000001 10090.ENSMUSP00000036031 0 0 0 58 181 0 85 232
-10090.ENSMUSP00000000001 10090.ENSMUSP00000039580 0 0 0 60 158 0 81 209
-10090.ENSMUSP00000000001 10090.ENSMUSP00000040516 0 0 0 0 196 0 0 196
+10090.ENSMUSP00000000001 10090.ENSMUSP00000012345 0 0 0 0 117 0 0 765
diff --git a/examples/data/string2.tsv b/examples/data/string2.tsv
index 2189088..d113f7e 100644
--- a/examples/data/string2.tsv
+++ b/examples/data/string2.tsv
@@ -4,7 +4,12 @@ protein1 protein2 neighborhood fusion cooccurence coexpression experimental data
 10090.ENSMUSP00000000001 10090.ENSMUSP00000061493 0 0 0 156 45 0 0 159
 10090.ENSMUSP00000000001 10090.ENSMUSP00000090329 0 0 0 0 196 0 0 196
 10090.ENSMUSP00000000001 10090.ENSMUSP00000026270 0 0 0 187 0 0 49 193
-10090.ENSMUSP00000000001 10090.ENSMUSP00000001115 0 0 0 0 119 0 148 218
+10090.ENSMUSP00000000001 10090.ENSMUSP00000001115 0 0 0 0 119 0 148 918
 10090.ENSMUSP00000000001 10090.ENSMUSP00000020101 0 0 0 0 181 0 85 218
 10090.ENSMUSP00000000001 10090.ENSMUSP00000063804 0 0 0 0 179 0 57 192
 10090.ENSMUSP00000000001 10090.ENSMUSP00000018012 0 0 0 65 220 0 100 286
+10090.ENSMUSP00000000001 10090.ENSMUSP00000033545 0 0 0 0 179 0 57 192
+10090.ENSMUSP00000000001 10090.ENSMUSP00000113105 0 0 0 0 179 0 417 500
+10090.ENSMUSP00000000001 10090.ENSMUSP00000036031 0 0 0 58 181 0 85 232
+10090.ENSMUSP00000000001 10090.ENSMUSP00000039580 0 0 0 60 158 0 81 209
+10090.ENSMUSP00000000001 10090.ENSMUSP00000040516 0 0 0 0 196 0 0 196
diff --git a/koza/cli_runner.py b/koza/cli_runner.py
index 1ff29ae..70bdddc 100644
--- a/koza/cli_runner.py
+++ b/koza/cli_runner.py
@@ -64,23 +64,24 @@ def transform_source(
         
     with open(source, 'r') as source_fh:
         source_config = PrimaryFileConfig(**yaml.load(source_fh, Loader=UniqueIncludeLoader))
-        if not source_config.name:
-            source_config.name = Path(source).stem
+        
+    if not source_config.name:
+        source_config.name = Path(source).stem
 
-        if not source_config.transform_code:
-            # look for it alongside the source conf as a .py file
-            source_config.transform_code = str(Path(source).parent / Path(source).stem) + '.py'
+    if not source_config.transform_code:
+        # look for it alongside the source conf as a .py file
+        source_config.transform_code = str(Path(source).parent / Path(source).stem) + '.py'
 
-        koza_source = Source(source_config, row_limit)
+    koza_source = Source(source_config, row_limit)
 
-        translation_table = get_translation_table(
-            global_table if global_table else source_config.global_table,
-            local_table if local_table else source_config.local_table,
-        )
+    translation_table = get_translation_table(
+        global_table if global_table else source_config.global_table,
+        local_table if local_table else source_config.local_table,
+    )
 
-        source_koza = set_koza_app(koza_source, translation_table, output_dir, output_format, schema)
-        source_koza.process_maps()
-        source_koza.process_sources()
+    source_koza = set_koza_app(koza_source, translation_table, output_dir, output_format, schema)
+    source_koza.process_maps()
+    source_koza.process_sources()
 
 
 def validate_file(
diff --git a/koza/io/reader/csv_reader.py b/koza/io/reader/csv_reader.py
index 3efbc59..84c3876 100644
--- a/koza/io/reader/csv_reader.py
+++ b/koza/io/reader/csv_reader.py
@@ -4,9 +4,9 @@
 from koza.model.config.source_config import FieldType, HeaderMode
 from koza.utils.log_utils import get_logger
 
-LOG = get_logger(__name__)
-# import logging
-# LOG = logging.getLogger(__name__)
+# LOG = get_logger(__name__)
+import logging
+LOG = logging.getLogger(__name__)
 
 
 FIELDTYPE_CLASS = {
@@ -112,6 +112,7 @@ def __next__(self) -> Dict[str, Any]:
 
         try:
             if self.line_count == self.row_limit:
+                LOG.debug("Row limit reached")
                 raise StopIteration
             else:
                 row = next(self.reader)
diff --git a/koza/main.py b/koza/main.py
index 4a743a0..db2139c 100755
--- a/koza/main.py
+++ b/koza/main.py
@@ -37,9 +37,8 @@ def transform(
     # os.path.splitext(os.path.basename(source))[0] # name of the yaml file without the yaml
     
     set_log_config(logging.INFO if (verbose is None) else logging.DEBUG if (verbose == True) else logging.WARNING)
-    logfile = Path(f"logs/{source.split('/')[1]}_{source.split('/')[2][:-5]}.log")
     logger = get_logger(__name__, verbose) if not logging.getLogger().hasHandlers() else logging.getLogger()
-    if log: fh = add_log_fh(logger, logfile)
+    if log: fh = add_log_fh(logger, f"logs/{Path(source).name}.log")
     
     output_path = Path(output_dir)
 
diff --git a/koza/utils/log_utils.py b/koza/utils/log_utils.py
index e16dd16..71d54ac 100644
--- a/koza/utils/log_utils.py
+++ b/koza/utils/log_utils.py
@@ -36,7 +36,7 @@ def get_logger(name: str, verbose: bool = None) -> logging.Logger:
 
     logger = logging.getLogger(name)
     logger.setLevel(log_level)
-    # logger.propagate = False
+    logger.propagate = False
 
     if not logger.hasHandlers():
         stream_handler = logging.StreamHandler(sys.stdout)
diff --git a/poetry.lock b/poetry.lock
index 52e646c..17373f3 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -61,7 +61,7 @@ pytz = ">=2015.7"
 
 [[package]]
 name = "biolink-model"
-version = "3.0.3"
+version = "3.1.0"
 description = "'A high level datamodel of biological entities and associations'"
 category = "dev"
 optional = false
@@ -222,7 +222,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "exceptiongroup"
-version = "1.0.0"
+version = "1.0.1"
 description = "Backport of PEP 654 (exception groups)"
 category = "dev"
 optional = false
@@ -291,7 +291,7 @@ test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>=
 
 [[package]]
 name = "greenlet"
-version = "2.0.0"
+version = "2.0.1"
 description = "Lightweight in-process concurrent programming"
 category = "main"
 optional = false
@@ -299,7 +299,7 @@ python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
 
 [package.extras]
 docs = ["Sphinx", "docutils (<0.18)"]
-test = ["faulthandler", "objgraph"]
+test = ["faulthandler", "objgraph", "psutil"]
 
 [[package]]
 name = "hbreader"
@@ -686,7 +686,7 @@ min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-imp
 
 [[package]]
 name = "mkdocs-material"
-version = "8.5.7"
+version = "8.5.9"
 description = "Documentation that simply works"
 category = "dev"
 optional = false
@@ -696,7 +696,7 @@ python-versions = ">=3.7"
 jinja2 = ">=3.0.2"
 markdown = ">=3.2"
 mkdocs = ">=1.4.0"
-mkdocs-material-extensions = ">=1.0.3"
+mkdocs-material-extensions = ">=1.1"
 pygments = ">=2.12"
 pymdown-extensions = ">=9.4"
 requests = ">=2.26"
@@ -814,15 +814,15 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "platformdirs"
-version = "2.5.2"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+version = "2.5.3"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx (>=4)", "sphinx-autodoc-typehints (>=1.12)"]
-test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
+docs = ["furo (>=2022.9.29)", "proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.4)"]
+test = ["appdirs (==1.4.4)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
 
 [[package]]
 name = "pluggy"
@@ -903,7 +903,7 @@ jsonasobj = ">=1.2.1"
 
 [[package]]
 name = "pymdown-extensions"
-version = "9.7"
+version = "9.8"
 description = "Extension pack for Python Markdown."
 category = "dev"
 optional = false
@@ -925,7 +925,7 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pyrsistent"
-version = "0.19.1"
+version = "0.19.2"
 description = "Persistent/Functional/Immutable data structures"
 category = "main"
 optional = false
@@ -1111,7 +1111,7 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "setuptools"
-version = "65.5.0"
+version = "65.5.1"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 category = "main"
 optional = false
@@ -1119,7 +1119,7 @@ python-versions = ">=3.7"
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mock", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
@@ -1297,7 +1297,7 @@ test = ["pytest"]
 
 [[package]]
 name = "sqlalchemy"
-version = "1.4.42"
+version = "1.4.43"
 description = "Database Abstraction Library"
 category = "main"
 optional = false
@@ -1450,8 +1450,8 @@ babel = [
     {file = "Babel-2.11.0.tar.gz", hash = "sha256:5ef4b3226b0180dedded4229651c8b0e1a3a6a2837d45a073272f313e4cf97f6"},
 ]
 biolink-model = [
-    {file = "biolink-model-3.0.3.tar.gz", hash = "sha256:1a1b00936bd56d36d9d2b957e28877043e59cfad1ce446c20721e5972fe68e04"},
-    {file = "biolink_model-3.0.3-py3-none-any.whl", hash = "sha256:9cc9e92c6c0a92f9099dd60635936d300558051420c15bb8d6b225ba005e0072"},
+    {file = "biolink-model-3.1.0.tar.gz", hash = "sha256:e6ba93ba0a61148e148f55aa2eccfa3154bcf676d7caa13a20505202041e9aac"},
+    {file = "biolink_model-3.1.0-py3-none-any.whl", hash = "sha256:ec765b64d4ab83bd8541bb81005f867f11b5ca29535fb4c6ac5fd8b5b408e5f7"},
 ]
 black = [
     {file = "black-22.3.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:2497f9c2386572e28921fa8bec7be3e51de6801f7459dffd6e62492531c47e09"},
@@ -1526,8 +1526,8 @@ et-xmlfile = [
     {file = "et_xmlfile-1.1.0.tar.gz", hash = "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c"},
 ]
 exceptiongroup = [
-    {file = "exceptiongroup-1.0.0-py3-none-any.whl", hash = "sha256:2ac84b496be68464a2da60da518af3785fff8b7ec0d090a581604bc870bdee41"},
-    {file = "exceptiongroup-1.0.0.tar.gz", hash = "sha256:affbabf13fb6e98988c38d9c5650e701569fe3c1de3233cfb61c5f33774690ad"},
+    {file = "exceptiongroup-1.0.1-py3-none-any.whl", hash = "sha256:4d6c0aa6dd825810941c792f53d7b8d71da26f5e5f84f20f9508e8f2d33b140a"},
+    {file = "exceptiongroup-1.0.1.tar.gz", hash = "sha256:73866f7f842ede6cb1daa42c4af078e2035e5f7607f0e2c762cc51bb31bbe7b2"},
 ]
 fsspec = [
     {file = "fsspec-2022.10.0-py3-none-any.whl", hash = "sha256:6b7c6ab3b476cdf17efcfeccde7fca28ef5a48f73a71010aaceec5fc15bf9ebf"},
@@ -1542,61 +1542,63 @@ graphviz = [
     {file = "graphviz-0.20.1.zip", hash = "sha256:8c58f14adaa3b947daf26c19bc1e98c4e0702cdc31cf99153e6f06904d492bf8"},
 ]
 greenlet = [
-    {file = "greenlet-2.0.0-cp27-cp27m-macosx_10_14_x86_64.whl", hash = "sha256:4be4dedbd2fa9b7c35627f322d6d3139cb125bc18d5ef2f40237990850ea446f"},
-    {file = "greenlet-2.0.0-cp27-cp27m-manylinux2010_x86_64.whl", hash = "sha256:75c022803de010294366f3608d4bba3e346693b1b7427b79d57e3d924ed03838"},
-    {file = "greenlet-2.0.0-cp27-cp27m-win32.whl", hash = "sha256:4a1953465b7651073cffde74ed7d121e602ef9a9740d09ee137b01879ac15a2f"},
-    {file = "greenlet-2.0.0-cp27-cp27m-win_amd64.whl", hash = "sha256:a65205e6778142528978b4acca76888e7e7f0be261e395664e49a5c21baa2141"},
-    {file = "greenlet-2.0.0-cp27-cp27mu-manylinux2010_x86_64.whl", hash = "sha256:d71feebf5c8041c80dfda76427e14e3ca00bca042481bd3e9612a9d57b2cbbf7"},
-    {file = "greenlet-2.0.0-cp310-cp310-macosx_10_15_x86_64.whl", hash = "sha256:f7edbd2957f72aea357241fe42ffc712a8e9b8c2c42f24e2ef5d97b255f66172"},
-    {file = "greenlet-2.0.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:79687c48e7f564be40c46b3afea6d141b8d66ffc2bc6147e026d491c6827954a"},
-    {file = "greenlet-2.0.0-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:a245898ec5e9ca0bc87a63e4e222cc633dc4d1f1a0769c34a625ad67edb9f9de"},
-    {file = "greenlet-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:adcf45221f253b3a681c99da46fa6ac33596fa94c2f30c54368f7ee1c4563a39"},
-    {file = "greenlet-2.0.0-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:3dc294afebf2acfd029373dbf3d01d36fd8d6888a03f5a006e2d690f66b153d9"},
-    {file = "greenlet-2.0.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:1cfeae4dda32eb5c64df05d347c4496abfa57ad16a90082798a2bba143c6c854"},
-    {file = "greenlet-2.0.0-cp310-cp310-win_amd64.whl", hash = "sha256:d58d4b4dc82e2d21ebb7dd7d3a6d370693b2236a1407fe3988dc1d4ea07575f9"},
-    {file = "greenlet-2.0.0-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:e0d7efab8418c1fb3ea00c4abb89e7b0179a952d0d53ad5fcff798ca7440f8e8"},
-    {file = "greenlet-2.0.0-cp311-cp311-win_amd64.whl", hash = "sha256:f8a10e14238407be3978fa6d190eb3724f9d766655fefc0134fd5482f1fb0108"},
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-    {file = "greenlet-2.0.0-cp35-cp35m-win_amd64.whl", hash = "sha256:cc211c2ff5d3b2ba8d557a71e3b4f0f0a2020067515143a9516ea43884271192"},
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-    {file = "greenlet-2.0.0-cp36-cp36m-win32.whl", hash = "sha256:eca9c0473de053dcc92156dd62c38c3578628b536c7f0cd66e655e211c14ac32"},
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-    {file = "greenlet-2.0.0-cp37-cp37m-macosx_10_15_x86_64.whl", hash = "sha256:6b28420ae290bfbf5d827f976abccc2f74f0a3f5e4fb69b66acf98f1cbe95e7e"},
-    {file = "greenlet-2.0.0-cp37-cp37m-manylinux2010_x86_64.whl", hash = "sha256:2b8e1c939b363292ecc93999fb1ad53ffc5d0aac8e933e4362b62365241edda5"},
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 ]
 stringcase = [
     {file = "stringcase-1.2.0.tar.gz", hash = "sha256:48a06980661908efe8d9d34eab2b6c13aefa2163b3ced26972902e3bdfd87008"},
diff --git a/pyproject.toml b/pyproject.toml
index 4b17f23..18ee02b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "koza"
-version = "0.2.2"
+version = "0.2.3"
 description = "Data transformation framework for LinkML data models"
 authors = [
     "The Monarch Initiative <info@monarchinitiative.org>",
diff --git a/tests/resources/multifile.yaml b/tests/resources/multifile.yaml
new file mode 100644
index 0000000..d41cb4a
--- /dev/null
+++ b/tests/resources/multifile.yaml
@@ -0,0 +1,35 @@
+name: 'protein-links-detailed'
+
+delimiter: ' '
+
+files:
+  - './examples/data/string.tsv'
+  - './examples/data/string2.tsv'
+
+metadata: !include './examples/string/metadata.yaml'
+
+columns: !include './examples/standards/string.yaml'
+
+filters:
+  - inclusion: 'include'
+    column: 'combined_score'
+    filter_code: 'lt'
+    value: 700
+
+transform_code: './examples/string/protein-links-detailed.py'
+
+transform_mode: 'loop'
+
+node_properties:
+  - 'id'
+  - 'category'
+  - 'provided_by'
+
+edge_properties:
+  - 'id'
+  - 'subject'
+  - 'predicate'
+  - 'object'
+  - 'category'
+  - 'relation'
+  - 'provided_by'
diff --git a/tests/unit/test_multifile.py b/tests/unit/test_multifile.py
new file mode 100644
index 0000000..a6a8806
--- /dev/null
+++ b/tests/unit/test_multifile.py
@@ -0,0 +1,22 @@
+import pytest
+import yaml
+from pathlib import Path
+
+from koza.model.source import Source
+from koza.model.config.source_config import PrimaryFileConfig
+from koza.io.yaml_loader import UniqueIncludeLoader
+
+def test_multiple_files():
+    source_file = Path(__file__).parent.parent / 'resources' / 'multifile.yaml'
+
+    row_limit = None
+    with open(source_file, 'r') as source_fh:
+        source_config = PrimaryFileConfig(**yaml.load(source_fh, Loader=UniqueIncludeLoader))
+        if not source_config.name:
+            source_config.name = Path(source_file).stem
+
+    source = Source(source_config, row_limit)
+
+    row_count = sum(1 for row in source)
+
+    assert row_count == 15