diff --git a/README.md b/README.md
index 7a5c818..1b248a0 100644
--- a/README.md
+++ b/README.md
@@ -10,6 +10,12 @@ poetry install
 poetry shell
 ```
 
+Alternative install with pip
+
+```shell
+pip install pheval-ai-marrvel
+```
+
 # Configuring a single run:
 
 ## Setting up the input directory
@@ -22,6 +28,7 @@ variant_analysis: True
 gene_analysis: True
 disease_analysis: False
 tool_specific_configuration_options:
+  environment: nextflow # either apptainer/docker/nextflow
 ```
 
 The AI-MARRVEL data dependencies should also be unpacked into the input directory. The overall structure of the input directory should look something like:
diff --git a/config.yaml b/config.yaml
index f0e86a8..3a93d8c 100644
--- a/config.yaml
+++ b/config.yaml
@@ -4,4 +4,4 @@ variant_analysis: True
 gene_analysis: True
 disease_analysis: False
 tool_specific_configuration_options:
-  environment: apptainer # either apptainer or docker
\ No newline at end of file
+  environment: nextflow # either apptainer/docker/nextflow
\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
index d731a6c..849a672 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -47,6 +47,25 @@ files = [
     {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
 ]
 
+[[package]]
+name = "arrow"
+version = "1.3.0"
+description = "Better dates & times for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"},
+    {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"},
+]
+
+[package.dependencies]
+python-dateutil = ">=2.7.0"
+types-python-dateutil = ">=2.8.10"
+
+[package.extras]
+doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
+test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"]
+
 [[package]]
 name = "astroid"
 version = "2.15.8"
@@ -68,22 +87,22 @@ wrapt = [
 
 [[package]]
 name = "attrs"
-version = "23.2.0"
+version = "24.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
-    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
+    {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
+    {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[tests]", "pre-commit"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
-tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
-tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
+benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 
 [[package]]
 name = "bcp47"
@@ -119,24 +138,24 @@ lxml = ["lxml"]
 
 [[package]]
 name = "casefy"
-version = "0.1.7"
+version = "1.0.0"
 description = "Utilities for string case conversion."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "casefy-0.1.7-py3-none-any.whl", hash = "sha256:ab05ff1c67f2a8e62d9f8986fa9a849416d61ac5413ec57d1f827b4f36589cf6"},
-    {file = "casefy-0.1.7.tar.gz", hash = "sha256:6accce985a64b9edb2a610a29ac489d78fac80e52ff8f2d137e294f2f92b8027"},
+    {file = "casefy-1.0.0-py3-none-any.whl", hash = "sha256:c89f96fb0fbd13691073b7a65c1e668e81453247d647479a3db105e86d7b0df9"},
+    {file = "casefy-1.0.0.tar.gz", hash = "sha256:bc99428475c2089c5f6a21297b4cfe4e83dff132cf3bb06655ddcb90632af1ed"},
 ]
 
 [[package]]
 name = "cattrs"
-version = "23.2.3"
+version = "24.1.2"
 description = "Composable complex class support for attrs and dataclasses."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "cattrs-23.2.3-py3-none-any.whl", hash = "sha256:0341994d94971052e9ee70662542699a3162ea1e0c62f7ce1b4a57f563685108"},
-    {file = "cattrs-23.2.3.tar.gz", hash = "sha256:a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f"},
+    {file = "cattrs-24.1.2-py3-none-any.whl", hash = "sha256:67c7495b760168d931a10233f979b28dc04daf853b30752246f4f8471c6d68d0"},
+    {file = "cattrs-24.1.2.tar.gz", hash = "sha256:8028cfe1ff5382df59dd36474a86e02d817b06eaf8af84555441bac915d2ef85"},
 ]
 
 [package.dependencies]
@@ -148,6 +167,7 @@ typing-extensions = {version = ">=4.1.0,<4.6.3 || >4.6.3", markers = "python_ver
 bson = ["pymongo (>=4.4.0)"]
 cbor2 = ["cbor2 (>=5.4.6)"]
 msgpack = ["msgpack (>=1.0.5)"]
+msgspec = ["msgspec (>=0.18.5)"]
 orjson = ["orjson (>=3.9.2)"]
 pyyaml = ["pyyaml (>=6.0)"]
 tomlkit = ["tomlkit (>=0.11.8)"]
@@ -155,15 +175,28 @@ ujson = ["ujson (>=5.7.0)"]
 
 [[package]]
 name = "certifi"
-version = "2024.6.2"
+version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"},
-    {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"},
+    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
+    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
 ]
 
+[[package]]
+name = "cfgraph"
+version = "0.2.1"
+description = "rdflib collections flattening graph"
+optional = false
+python-versions = "*"
+files = [
+    {file = "CFGraph-0.2.1.tar.gz", hash = "sha256:b57fe7044a10b8ff65aa3a8a8ddc7d4cd77bf511b42e57289cd52cbc29f8fe74"},
+]
+
+[package.dependencies]
+rdflib = ">=0.4.2"
+
 [[package]]
 name = "chardet"
 version = "5.2.0"
@@ -177,122 +210,137 @@ files = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
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-version = "0.4.3"
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 description = "Lookup and instantiate classes with style."
 optional = false
-python-versions = ">=3.7"
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 [package.extras]
 click = ["click"]
-docdata = ["docdata"]
-docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-rtd-theme"]
+docs = ["sphinx (<8)", "sphinx-automodapi", "sphinx-rtd-theme"]
 numpy = ["numpy"]
 optuna = ["optuna"]
 ray = ["ray[tune] (<2.0.0)"]
 sklearn = ["scikit-learn"]
+tabulate = ["tabulate"]
 tests = ["coverage", "docdata", "pytest"]
 torch = ["torch"]
 torch-geometric = ["torch", "torch-geometric", "torch-sparse"]
@@ -324,66 +372,76 @@ files = [
 
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+]
+
+[package.dependencies]
+numpy = ">=1.23"
 
 [package.extras]
 bokeh = ["bokeh", "selenium"]
 docs = ["furo", "sphinx (>=7.2)", "sphinx-copybutton"]
-mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.8.0)", "types-Pillow"]
+mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.11.1)", "types-Pillow"]
 test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
-test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
+test-no-images = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist", "wurlitzer"]
 
 [[package]]
 name = "coverage"
@@ -449,27 +507,26 @@ toml = ["tomli"]
 
 [[package]]
 name = "curies"
-version = "0.7.9"
-description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
+version = "0.9.0"
+description = "Idiomatic conversion between URIs and compact URIs (CURIEs)"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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+    {file = "curies-0.9.0.tar.gz", hash = "sha256:f630fa05b31aff144da66ace18a2c25b30adfa859df36e5fbd8b633b43c80d3a"},
 ]
 
 [package.dependencies]
-pydantic = "*"
+pydantic = ">=2.0"
 pytrie = "*"
-requests = "*"
 
 [package.extras]
-docs = ["sphinx", "sphinx-automodapi", "sphinx-rtd-theme"]
+docs = ["sphinx (>=8)", "sphinx-automodapi", "sphinx-rtd-theme (>=3.0)"]
 fastapi = ["defusedxml", "fastapi", "httpx", "python-multipart", "uvicorn"]
 flask = ["defusedxml", "flask"]
 pandas = ["pandas"]
 rdflib = ["rdflib"]
-tests = ["coverage", "pytest"]
+tests = ["coverage", "pytest", "requests"]
 
 [[package]]
 name = "cycler"
@@ -499,20 +556,20 @@ files = [
 
 [[package]]
 name = "deprecated"
-version = "1.2.14"
+version = "1.2.15"
 description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
 files = [
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+    {file = "Deprecated-1.2.15-py2.py3-none-any.whl", hash = "sha256:353bc4a8ac4bfc96800ddab349d89c25dec1079f65fd53acdcc1e0b975b21320"},
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 ]
 
 [package.dependencies]
 wrapt = ">=1.10,<2"
 
 [package.extras]
-dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
+dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "jinja2 (>=3.0.3,<3.1.0)", "setuptools", "sphinx (<2)", "tox"]
 
 [[package]]
 name = "deprecation"
@@ -530,13 +587,13 @@ packaging = "*"
 
 [[package]]
 name = "dill"
-version = "0.3.8"
+version = "0.3.9"
 description = "serialize all of Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "dill-0.3.8.tar.gz", hash = "sha256:3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca"},
+    {file = "dill-0.3.9-py3-none-any.whl", hash = "sha256:468dff3b89520b474c0397703366b7b95eebe6303f108adf9b19da1f702be87a"},
+    {file = "dill-0.3.9.tar.gz", hash = "sha256:81aa267dddf68cbfe8029c42ca9ec6a4ab3b22371d1c450abc54422577b4512c"},
 ]
 
 [package.extras]
@@ -565,6 +622,78 @@ docs = ["myst-parser (==0.18.0)", "sphinx (==5.1.1)"]
 ssh = ["paramiko (>=2.4.3)"]
 websockets = ["websocket-client (>=1.3.0)"]
 
+[[package]]
+name = "duckdb"
+version = "1.1.3"
+description = "DuckDB in-process database"
+optional = false
+python-versions = ">=3.7.0"
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 unicode = ["unicodedata2 (>=15.1.0)"]
 woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
+[[package]]
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+optional = false
+python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4"
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 [[package]]
 name = "funowl"
 version = "0.2.3"
@@ -751,71 +899,102 @@ files = [
 [package.dependencies]
 beautifulsoup4 = "*"
 
+[[package]]
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+test = ["coverage", "pytest (>=7,<8.1)", "pytest-cov", "pytest-mock (>=3)"]
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+
 [[package]]
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 name = "iniconfig"
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 [package.dependencies]
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 [[package]]
 name = "isort"
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 [package.dependencies]
@@ -1137,36 +1345,82 @@ files = [
 [package.dependencies]
 attrs = ">=19.2.0"
 
+[[package]]
+name = "jsonpatch"
+version = "1.33"
+description = "Apply JSON-Patches (RFC 6902)"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
+files = [
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+    {file = "jsonpatch-1.33.tar.gz", hash = "sha256:9fcd4009c41e6d12348b4a0ff2563ba56a2923a7dfee731d004e212e1ee5030c"},
+]
+
+[package.dependencies]
+jsonpointer = ">=1.9"
+
+[[package]]
+name = "jsonpath-ng"
+version = "1.7.0"
+description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming."
+optional = false
+python-versions = "*"
+files = [
+    {file = "jsonpath-ng-1.7.0.tar.gz", hash = "sha256:f6f5f7fd4e5ff79c785f1573b394043b39849fb2bb47bcead935d12b00beab3c"},
+]
+
+[package.dependencies]
+ply = "*"
+
+[[package]]
+name = "jsonpointer"
+version = "3.0.0"
+description = "Identify specific nodes in a JSON document (RFC 6901)"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "jsonpointer-3.0.0-py2.py3-none-any.whl", hash = "sha256:13e088adc14fca8b6aa8177c044e12701e6ad4b28ff10e65f2267a90109c9942"},
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+]
+
 [[package]]
 name = "jsonschema"
-version = "4.22.0"
+version = "4.23.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"},
 ]
 
 [package.dependencies]
 attrs = ">=22.2.0"
+fqdn = {version = "*", optional = true, markers = "extra == \"format\""}
+idna = {version = "*", optional = true, markers = "extra == \"format\""}
+isoduration = {version = "*", optional = true, markers = "extra == \"format\""}
+jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format\""}
 jsonschema-specifications = ">=2023.03.6"
 referencing = ">=0.28.4"
+rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format\""}
+rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""}
 rpds-py = ">=0.7.1"
+uri-template = {version = "*", optional = true, markers = "extra == \"format\""}
+webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format\""}
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
-format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=24.6.0)"]
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2023.12.1"
+version = "2024.10.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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+    {file = "jsonschema_specifications-2024.10.1-py3-none-any.whl", hash = "sha256:a09a0680616357d9a0ecf05c12ad234479f549239d0f5b55f3deea67475da9bf"},
+    {file = "jsonschema_specifications-2024.10.1.tar.gz", hash = "sha256:0f38b83639958ce1152d02a7f062902c41c8fd20d558b0c34344292d417ae272"},
 ]
 
 [package.dependencies]
@@ -1189,13 +1443,13 @@ linkml-runtime = ">=1.1.24"
 
 [[package]]
 name = "kgcl-schema"
-version = "0.6.8"
+version = "0.6.9"
 description = "Schema for the KGCL project."
 optional = false
 python-versions = "<4.0,>=3.9"
 files = [
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+    {file = "kgcl_schema-0.6.9.tar.gz", hash = "sha256:1bb0f9f13356df7b5c6ba9c73a7124dc897e525af49f40454dafd45bfca021bd"},
 ]
 
 [package.dependencies]
@@ -1206,126 +1460,136 @@ prefixmaps = ">=0.2.0,<0.3.0"
 
 [[package]]
 name = "kiwisolver"
-version = "1.4.5"
+version = "1.4.7"
 description = "A fast implementation of the Cassowary constraint solver"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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@@ -1399,13 +1724,13 @@ pydantic = "*"
 
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 ]
 
 [package.extras]
@@ -1575,113 +1900,126 @@ cssselect = ["cssselect (>=0.7)"]
 html-clean = ["lxml-html-clean"]
 html5 = ["html5lib"]
 htmlsoup = ["BeautifulSoup4"]
-source = ["Cython (>=3.0.10)"]
+source = ["Cython (>=3.0.11)"]
 
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+version = "0.6.18"
 description = "Ontology Access Kit: Python library for common ontology operations over a variety of backends"
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 python-versions = "<4.0.0,>=3.9"
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 [package.dependencies]
@@ -1838,15 +2196,15 @@ appdirs = ">=1.4.4"
 class-resolver = ">=0.4.2"
 click = "*"
 curies = ">=0.6.6"
-defusedxml = ">=0.7.1,<0.8.0"
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 eutils = ">=0.6.0"
 funowl = ">=0.2.0"
-jsonlines = ">=4.0.0,<5.0.0"
+jsonlines = "*"
 kgcl-rdflib = "0.5.0"
-kgcl-schema = ">=0.6.8,<0.7.0"
+kgcl-schema = ">=0.6.9,<0.7.0"
 linkml-renderer = ">=0.3.0"
 linkml-runtime = ">=1.5.3"
-ndex2 = ">=3.5.0,<4.0.0"
+ndex2 = ">=3.5.0"
 networkx = ">=2.7.1"
 ols-client = ">=0.1.1"
 ontoportal-client = ">=0.0.3"
@@ -1861,12 +2219,12 @@ semsql = ">=0.3.1"
 SPARQLWrapper = "*"
 SQLAlchemy = ">=1.4.32"
 sssom = ">=0.4.4,<0.5.0"
-tenacity = ">=8.2.3,<9.0.0"
+tenacity = ">=8.2.3"
 
 [package.extras]
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-llm = ["aiohttp", "html2text", "llm"]
-semsimian = ["semsimian (>=0.2.16)"]
+llm = ["aiohttp", "html2text", "llm (>=0.14,<0.15)"]
+semsimian = ["semsimian (>=0.2.18)"]
 
 [[package]]
 name = "ols-client"
@@ -1909,53 +2267,80 @@ typing-extensions = "*"
 docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-rtd-theme"]
 tests = ["coverage", "pytest", "unittest-templates"]
 
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+
+[package.dependencies]
+et-xmlfile = "*"
+
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@@ -2010,34 +2395,49 @@ pandas = "*"
 sqlalchemy = "*"
 
 [[package]]
-name = "phenopackets"
-version = "2.0.2.post1"
-description = "A python implementation of phenopackets protobuf"
+name = "parse"
+version = "1.20.2"
+description = "parse() is the opposite of format()"
 optional = false
 python-versions = "*"
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+]
+
+[[package]]
+name = "phenopackets"
+version = "2.0.2.post4"
+description = "Phenopacket Schema"
+optional = false
+python-versions = ">=3.8"
+files = [
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+protobuf = ">=3.20.2,<4.0.0"
+
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+version = "0.4.1"
 description = ""
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 google = ">=3.0.0,<4.0.0"
 jaydebeapi = ">=1.2.3"
 matplotlib = ">=3.7.0,<4.0.0"
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+    {file = "pillow-11.0.0.tar.gz", hash = "sha256:72bacbaf24ac003fea9bff9837d1eedb6088758d41e100c1552930151f677739"},
 ]
 
 [package.extras]
-docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-removed-in", "sphinxext-opengraph"]
+docs = ["furo", "olefile", "sphinx (>=8.1)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
 fpx = ["olefile"]
 mic = ["olefile"]
 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
@@ -2140,29 +2546,29 @@ xmp = ["defusedxml"]
 
 [[package]]
 name = "platformdirs"
-version = "4.2.2"
+version = "4.3.6"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "platformdirs-4.3.6.tar.gz", hash = "sha256:357fb2acbc885b0419afd3ce3ed34564c13c9b95c89360cd9563f73aa5e2b907"},
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-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"]
-type = ["mypy (>=1.8)"]
+docs = ["furo (>=2024.8.6)", "proselint (>=0.14)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)"]
+type = ["mypy (>=1.11.2)"]
 
 [[package]]
 name = "plotly"
-version = "5.22.0"
+version = "5.24.1"
 description = "An open-source, interactive data visualization library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2184,6 +2590,17 @@ files = [
 dev = ["pre-commit", "tox"]
 testing = ["pytest", "pytest-benchmark"]
 
+[[package]]
+name = "ply"
+version = "3.11"
+description = "Python Lex & Yacc"
+optional = false
+python-versions = "*"
+files = [
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+]
+
 [[package]]
 name = "polars"
 version = "0.19.19"
@@ -2239,13 +2656,13 @@ requests = ">=2.28.1,<3.0.0"
 
 [[package]]
 name = "prefixmaps"
-version = "0.2.4"
+version = "0.2.6"
 description = "A python library for retrieving semantic prefix maps"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2254,13 +2671,13 @@ pyyaml = ">=5.3.1"
 
 [[package]]
 name = "pronto"
-version = "2.5.7"
+version = "2.5.8"
 description = "Python frontend to ontologies."
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -2316,120 +2733,142 @@ PyYAML = "*"
 
 [[package]]
 name = "pycodestyle"
-version = "2.11.1"
+version = "2.12.1"
 description = "Python style guide checker"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "pydantic"
-version = "2.7.3"
+version = "2.10.2"
 description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
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-pydantic-core = "2.18.4"
-typing-extensions = ">=4.6.1"
+annotated-types = ">=0.6.0"
+pydantic-core = "2.27.1"
+typing-extensions = ">=4.12.2"
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
+timezone = ["tzdata"]
 
 [[package]]
 name = "pydantic-core"
-version = "2.18.4"
+version = "2.27.1"
 description = "Core functionality for Pydantic validation and serialization"
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 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -2480,13 +2919,13 @@ testutils = ["gitpython (>3)"]
 
 [[package]]
 name = "pyparsing"
-version = "3.1.2"
+version = "3.2.0"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
-python-versions = ">=3.6.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.extras]
@@ -2516,44 +2955,87 @@ orjson = ["orjson"]
 toml = ["tomli", "tomli-w"]
 yaml = ["pyyaml"]
 
+[[package]]
+name = "pyshex"
+version = "0.8.1"
+description = "Python ShEx Implementation"
+optional = false
+python-versions = ">=3.6"
+files = [
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+sparqlwrapper = ">=1.8.5"
+urllib3 = "*"
+
+[[package]]
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+version = "0.9.1"
+description = "PyShExC - Python ShEx compiler"
+optional = false
+python-versions = ">=3.7"
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+
 [[package]]
 name = "pysolr"
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 description = "Lightweight Python client for Apache Solr"
 optional = false
 python-versions = "*"
 files = [
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 requests = ">=2.9.1"
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 [package.extras]
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 ]
 
 [package.dependencies]
 click = "*"
 requests = "*"
 tqdm = "*"
+typing-extensions = "*"
 
 [package.extras]
 aws = ["boto3"]
-docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
+docs = ["sphinx (>=8)", "sphinx-click", "sphinx-rtd-theme (>=3.0)", "sphinx_automodapi"]
 pandas = ["pandas"]
 rdf = ["rdflib"]
-tests = ["coverage", "pytest", "requests-file"]
+tests = ["coverage", "pytest", "requests_file"]
 xml = ["lxml"]
 
 [[package]]
@@ -2621,96 +3103,102 @@ sortedcontainers = "*"
 
 [[package]]
 name = "pytz"
-version = "2024.1"
+version = "2024.2"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
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 name = "pywin32"
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 [[package]]
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 name = "seaborn"
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 linkml-runtime = ">=1.2.15,<2.0.0"
 SQLAlchemy-Utils = ">=0.38.2,<0.39.0"
 
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+
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 version = "1.16.0"
@@ -3120,15 +3724,31 @@ files = [
 
 [[package]]
 name = "soupsieve"
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+
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 version = "2.0.0"
@@ -3151,64 +3771,72 @@ pandas = ["pandas (>=1.3.5)"]
 
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 typing-extensions = ">=4.6.0"
 
 [package.extras]
@@ -3217,7 +3845,7 @@ aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
 aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
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-mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"]
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 mssql = ["pyodbc"]
 mssql-pymssql = ["pymssql"]
 mssql-pyodbc = ["pyodbc"]
@@ -3266,13 +3894,13 @@ url = ["furl (>=0.4.1)"]
 
 [[package]]
 name = "sssom"
-version = "0.4.9"
+version = "0.4.13"
 description = "Operations on SSSOM mapping tables"
 optional = false
-python-versions = "<4.0,>=3.8"
+python-versions = "<4.0.0,>=3.9"
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 ]
 
 [package.dependencies]
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 curies = ">=0.7.3"
 deprecation = ">=2.1.0,<3.0.0"
 importlib-resources = ">=6.1.1,<7.0.0"
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 linkml-runtime = ">=1.7.5,<2.0.0"
 networkx = {version = ">=3.1", extras = ["networkx"]}
 pandas = ">1.0.3"
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 scipy = {version = "*", extras = ["scipy"]}
 sparqlwrapper = ">=2.0.0"
-sssom-schema = ">=0.15.2,<0.16.0"
+sssom-schema = ">=1.0.0,<2.0.0"
 validators = ">=0.20.0"
 
 [[package]]
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-version = "0.15.2"
+version = "1.0.0"
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 optional = false
-python-versions = "<4.0,>=3.8"
+python-versions = "<4.0.0,>=3.8.1"
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 ]
 
 [package.dependencies]
@@ -3307,13 +3936,13 @@ linkml-runtime = "*"
 
 [[package]]
 name = "tenacity"
-version = "8.3.0"
+version = "9.0.0"
 description = "Retry code until it succeeds"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.extras]
@@ -3333,46 +3962,88 @@ files = [
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.2.1"
 description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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 description = "Style preserving TOML library"
 optional = false
-python-versions = ">=3.7"
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 optional = false
 python-versions = ">=3.7"
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 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
-dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
+dev = ["nbval", "pytest (>=6)", "pytest-asyncio (>=0.24)", "pytest-cov", "pytest-timeout"]
+discord = ["requests"]
 notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
 
+[[package]]
+name = "types-python-dateutil"
+version = "2.9.0.20241003"
+description = "Typing stubs for python-dateutil"
+optional = false
+python-versions = ">=3.8"
+files = [
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 version = "4.12.2"
@@ -3401,15 +4072,29 @@ typing-extensions = ">=3.7.4"
 
 [[package]]
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 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
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 ]
 
+[[package]]
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+version = "1.3.0"
+description = "RFC 6570 URI Template Processor"
+optional = false
+python-versions = ">=3.7"
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+
 [[package]]
 name = "url-normalize"
 version = "1.4.3"
@@ -3426,13 +4111,13 @@ six = "*"
 
 [[package]]
 name = "urllib3"
-version = "2.2.1"
+version = "2.2.3"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.extras]
@@ -3443,95 +4128,146 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
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+version = "0.34.0"
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+[package.extras]
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+
+[[package]]
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 ]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "01e108b3f784e670f20502355de3aa083c96ece341a46028d8da747862435d9b"
+content-hash = "db17ac4f3f62c6f2a23551e658874e3143c0e0bd8fce87d230b8134c4c05d743"
diff --git a/pyproject.toml b/pyproject.toml
index d55faa3..be829d3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pheval-ai-marrvel"
-version = "0.1.5"
+version = "0.1.6"
 description = ""
 authors = ["Yasemin Bridges <y.bridges@qmul.ac.uk>"]
 readme = "README.md"
@@ -9,7 +9,7 @@ packages = [{include = "pheval_ai_marrvel", from = "src"}]
 [tool.poetry.dependencies]
 python = "^3.10"
 docker = "^7.1.0"
-pheval = "^0.3.8"
+pheval = "^0.4.0"
 
 [tool.poetry.scripts]
 pheval-ai = "pheval_ai_marrvel.cli:main"
diff --git a/src/pheval_ai_marrvel/run/prepare_next_flow_commands.py b/src/pheval_ai_marrvel/run/prepare_next_flow_commands.py
new file mode 100644
index 0000000..00b6c30
--- /dev/null
+++ b/src/pheval_ai_marrvel/run/prepare_next_flow_commands.py
@@ -0,0 +1,105 @@
+from dataclasses import dataclass
+from pathlib import Path
+from typing import List
+
+from pheval.utils.file_utils import all_files
+from pheval.utils.phenopacket_utils import PhenopacketUtil, phenopacket_reader
+
+
+@dataclass
+class NextFlowParameters:
+    """
+    Parameters for running AI MARRVEL with next flow.
+    Attributes:
+        executable (Path): Path to the executable.
+        ref_dir (Path): Path to the reference directory.
+        input_vcf (Path): Path to the input vcf file.
+        input_hpo (Path): Path to the input hpo file.
+        output_dir (Path): Path to the output directory.
+        sample_id (str): Sample ID.
+        reference_version (str): Genome reference version.
+    """
+
+    executable: Path
+    ref_dir: Path
+    input_vcf: Path
+    input_hpo: Path
+    output_dir: Path
+    sample_id: str
+    reference_version: str
+
+
+def get_next_flow_parameters(
+    phenopacket_path: Path, testdata_dir: Path, input_dir: Path, output_dir: Path
+):
+    """
+    Get next flow parameters for a sample.
+    Args:
+        phenopacket_path (Path): Path to the phenopacket file.
+        testdata_dir (Path): Path to the test data directory.
+        input_dir (Path): Path to the input directory.
+        output_dir (Path): Path to the output directory.
+    """
+    phenopacket = phenopacket_reader(phenopacket_path)
+    vcf_file_data = PhenopacketUtil(phenopacket).vcf_file_data(
+        phenopacket_path, testdata_dir.joinpath("vcf")
+    )
+    return NextFlowParameters(
+        executable=input_dir.joinpath("AI_MARRVEL/main.nf"),
+        ref_dir=input_dir,
+        input_vcf=vcf_file_data.uri,
+        input_hpo=testdata_dir.joinpath(f"hpo_ids/{phenopacket_path.stem}.txt"),
+        output_dir=output_dir,
+        sample_id=phenopacket.subject.id,
+        reference_version=vcf_file_data.file_attributes["genomeAssembly"],
+    )
+
+
+def create_next_flow_command(next_flow_parameters: NextFlowParameters) -> str:
+    return (
+        f"nextflow run {next_flow_parameters.executable} "
+        f"--ref-dir {next_flow_parameters.ref_dir} "
+        f"--input-vcf {next_flow_parameters.input_vcf} "
+        f"--input-hpo {next_flow_parameters.input_hpo} "
+        f"--outdir {next_flow_parameters.output_dir} "
+        f"--run-id {next_flow_parameters.sample_id} "
+        f"--ref-ver {next_flow_parameters.reference_version}"
+    )
+
+
+def write_commands(commands: List[str], tool_input_commands_dir: Path, testdata_dir: Path) -> None:
+    """
+    Write commands to a txt file.
+
+    Args:
+        commands (List[str]): The commands to write.
+        tool_input_commands_dir (Path): The tool input commands directory.
+        testdata_dir (Path): The testdata directory.
+    """
+    joined_commands_str = "\n".join(commands)
+    with open(
+        f"{tool_input_commands_dir.joinpath(f'{testdata_dir.name}_commands.txt')}", "w"
+    ) as commands_file:
+        commands_file.write(joined_commands_str)
+    commands_file.close()
+
+
+def create_nextflow_commands(
+    tool_input_commands_dir: Path, testdata_dir: Path, input_dir: Path, output_dir: Path
+) -> None:
+    """
+    Create nextflow commands for running AI-MARRVEL with a corpus.
+
+    Args:
+        tool_input_commands_dir (Path): The tool input commands directory.
+        testdata_dir (Path): The testdata directory.
+        input_dir (Path): The input directory.
+        output_dir (Path): The output directory.
+    """
+    all_commands = []
+    for phenopacket_path in all_files(testdata_dir.joinpath("phenopackets")):
+        next_flow_arguments = get_next_flow_parameters(
+            phenopacket_path, testdata_dir, input_dir, output_dir
+        )
+        all_commands.append(create_next_flow_command(next_flow_arguments))
+    write_commands(all_commands, tool_input_commands_dir, testdata_dir)
diff --git a/src/pheval_ai_marrvel/run/run.py b/src/pheval_ai_marrvel/run/run.py
index 333dff4..216e13d 100644
--- a/src/pheval_ai_marrvel/run/run.py
+++ b/src/pheval_ai_marrvel/run/run.py
@@ -3,6 +3,21 @@
 
 from pheval_ai_marrvel.run.create_apptainer_commands import create_apptainer_commands
 from pheval_ai_marrvel.run.create_docker_commands import run_docker
+from pheval_ai_marrvel.run.prepare_next_flow_commands import create_nextflow_commands
+
+
+def run_batch_file(testdata_dir: Path, tool_input_commands_dir: Path):
+    """
+    Run the batch file for the corpus.
+    Args:
+        testdata_dir (Path): Path to the test data directory.
+        tool_input_commands_dir (Path): Path to the input commands directory.
+    """
+    batch_file = tool_input_commands_dir.joinpath(f"{testdata_dir.name}_commands.txt")
+    subprocess.run(
+        ["bash", str(batch_file)],
+        shell=False,
+    )
 
 
 def run_commands(
@@ -21,12 +36,11 @@ def run_commands(
         input_dir (Path): Path to the input directory.
         output_dir (Path): Path to the output directory.
     """
-    if environment == "apptainer":
+    if environment.lower() == "apptainer":
         create_apptainer_commands(tool_input_commands_dir, testdata_dir, input_dir, output_dir)
-        batch_file = tool_input_commands_dir.joinpath(f"{testdata_dir.name}_commands.txt")
-        subprocess.run(
-            ["bash", str(batch_file)],
-            shell=False,
-        )
-    elif environment == "docker":
+        run_batch_file(testdata_dir, tool_input_commands_dir)
+    elif environment.lower() == "docker":
         run_docker(testdata_dir, input_dir, output_dir)
+    elif environment.lower() == "nextflow":
+        create_nextflow_commands(tool_input_commands_dir, testdata_dir, input_dir, output_dir)
+        run_batch_file(testdata_dir, tool_input_commands_dir)