diff --git a/poetry.lock b/poetry.lock
index e6023b80..666a4455 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -67,13 +67,13 @@ files = [
 
 [[package]]
 name = "bids-validator"
-version = "1.12.0"
+version = "1.13.1"
 description = "Validator for the Brain Imaging Data Structure"
 optional = false
 python-versions = "*"
 files = [
-    {file = "bids-validator-1.12.0.tar.gz", hash = "sha256:5f9ebd379cdf6d383e983c10539886bf5ea488e4ebf2bc21293125f510893116"},
-    {file = "bids_validator-1.12.0-py2.py3-none-any.whl", hash = "sha256:7936e9f31960cfbfe9af49b33e8d10999d7497d7fcd313d91ea3eda541ae4500"},
+    {file = "bids-validator-1.13.1.tar.gz", hash = "sha256:7205ce4e68fba172215332c786f1ac1665025b702b6dff2b1e158f00a2df9890"},
+    {file = "bids_validator-1.13.1-py2.py3-none-any.whl", hash = "sha256:da6edf5e76ef86c8a63b3fcee1dbfb039a16a9ef63cb0d2d05312c200d4607f7"},
 ]
 
 [[package]]
@@ -92,33 +92,33 @@ chardet = ">=3.0.2"
 
 [[package]]
 name = "black"
-version = "23.7.0"
+version = "23.9.1"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "black-23.9.1-cp38-cp38-macosx_10_16_x86_64.whl", hash = "sha256:cf3a4d00e4cdb6734b64bf23cd4341421e8953615cba6b3670453737a72ec204"},
+    {file = "black-23.9.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:cf99f3de8b3273a8317681d8194ea222f10e0133a24a7548c73ce44ea1679377"},
+    {file = "black-23.9.1-cp38-cp38-win_amd64.whl", hash = "sha256:14f04c990259576acd093871e7e9b14918eb28f1866f91968ff5524293f9c573"},
+    {file = "black-23.9.1-cp39-cp39-macosx_10_16_arm64.whl", hash = "sha256:c619f063c2d68f19b2d7270f4cf3192cb81c9ec5bc5ba02df91471d0b88c4c5c"},
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+    {file = "black-23.9.1-cp39-cp39-macosx_10_16_x86_64.whl", hash = "sha256:c46767e8df1b7beefb0899c4a95fb43058fa8500b6db144f4ff3ca38eb2f6393"},
+    {file = "black-23.9.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:50254ebfa56aa46a9fdd5d651f9637485068a1adf42270148cd101cdf56e0ad9"},
+    {file = "black-23.9.1-cp39-cp39-win_amd64.whl", hash = "sha256:403397c033adbc45c2bd41747da1f7fc7eaa44efbee256b53842470d4ac5a70f"},
+    {file = "black-23.9.1-py3-none-any.whl", hash = "sha256:6ccd59584cc834b6d127628713e4b6b968e5f79572da66284532525a042549f9"},
+    {file = "black-23.9.1.tar.gz", hash = "sha256:24b6b3ff5c6d9ea08a8888f6977eae858e1f340d7260cf56d70a49823236b62d"},
 ]
 
 [package.dependencies]
@@ -128,7 +128,7 @@ packaging = ">=22.0"
 pathspec = ">=0.9.0"
 platformdirs = ">=2"
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
-typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
+typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
@@ -357,6 +357,33 @@ pyyaml = ">=5.3.1"
 requests = ">=2.23.0"
 rich = "*"
 
+[[package]]
+name = "copier"
+version = "8.1.0"
+description = "A library for rendering project templates."
+optional = false
+python-versions = ">=3.7,<4.0"
+files = [
+    {file = "copier-8.1.0-py3-none-any.whl", hash = "sha256:56537163b1b24441a63504ebf56b8db588dee20b48ef4fc374a6c5a2b43010c1"},
+    {file = "copier-8.1.0.tar.gz", hash = "sha256:902b4eb65fafe7a1621991234d2ebf3bc3fc9323e64e3a2560a00c05c73f6229"},
+]
+
+[package.dependencies]
+colorama = ">=0.4.3"
+decorator = ">=5.1.1"
+dunamai = ">=1.7.0"
+funcy = ">=1.17"
+jinja2 = ">=3.1.1"
+jinja2-ansible-filters = ">=1.3.1"
+packaging = ">=23.0"
+pathspec = ">=0.9.0"
+plumbum = ">=1.6.9"
+pydantic = ">=1.10.2,<2"
+pygments = ">=2.7.1"
+pyyaml = ">=5.3.1"
+pyyaml-include = ">=1.2"
+questionary = ">=1.8.1"
+
 [[package]]
 name = "datrie"
 version = "0.8.2"
@@ -391,6 +418,17 @@ files = [
     {file = "datrie-0.8.2.tar.gz", hash = "sha256:525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d"},
 ]
 
+[[package]]
+name = "decorator"
+version = "5.1.1"
+description = "Decorators for Humans"
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
+    {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
+]
+
 [[package]]
 name = "distlib"
 version = "0.3.7"
@@ -434,6 +472,20 @@ files = [
     {file = "dpath-2.1.6.tar.gz", hash = "sha256:f1e07c72e8605c6a9e80b64bc8f42714de08a789c7de417e49c3f87a19692e47"},
 ]
 
+[[package]]
+name = "dunamai"
+version = "1.18.0"
+description = "Dynamic version generation"
+optional = false
+python-versions = ">=3.5,<4.0"
+files = [
+    {file = "dunamai-1.18.0-py3-none-any.whl", hash = "sha256:f9284a9f4048f0b809d11539896e78bde94c05b091b966a04a44ab4c48df03ce"},
+    {file = "dunamai-1.18.0.tar.gz", hash = "sha256:5200598561ea5ba956a6174c36e402e92206c6a6aa4a93a6c5cb8003ee1e0997"},
+]
+
+[package.dependencies]
+packaging = ">=20.9"
+
 [[package]]
 name = "exceptiongroup"
 version = "1.1.3"
@@ -464,18 +516,19 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 
 [[package]]
 name = "filelock"
-version = "3.12.2"
+version = "3.12.4"
 description = "A platform independent file lock."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "filelock-3.12.2-py3-none-any.whl", hash = "sha256:cbb791cdea2a72f23da6ac5b5269ab0a0d161e9ef0100e653b69049a7706d1ec"},
-    {file = "filelock-3.12.2.tar.gz", hash = "sha256:002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81"},
+    {file = "filelock-3.12.4-py3-none-any.whl", hash = "sha256:08c21d87ded6e2b9da6728c3dff51baf1dcecf973b768ef35bcbc3447edb9ad4"},
+    {file = "filelock-3.12.4.tar.gz", hash = "sha256:2e6f249f1f3654291606e046b09f1fd5eac39b360664c27f5aad072012f8bcbd"},
 ]
 
 [package.extras]
-docs = ["furo (>=2023.5.20)", "sphinx (>=7.0.1)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "diff-cover (>=7.5)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.7.26)", "sphinx (>=7.1.2)", "sphinx-autodoc-typehints (>=1.24)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-timeout (>=2.1)"]
+typing = ["typing-extensions (>=4.7.1)"]
 
 [[package]]
 name = "formulaic"
@@ -502,6 +555,17 @@ wrapt = ">=1.0"
 arrow = ["pyarrow (>=1)"]
 calculus = ["sympy (>=1.3,<1.10)"]
 
+[[package]]
+name = "funcy"
+version = "2.0"
+description = "A fancy and practical functional tools"
+optional = false
+python-versions = "*"
+files = [
+    {file = "funcy-2.0-py2.py3-none-any.whl", hash = "sha256:53df23c8bb1651b12f095df764bfb057935d49537a56de211b098f4c79614bb0"},
+    {file = "funcy-2.0.tar.gz", hash = "sha256:3963315d59d41c6f30c04bc910e10ab50a3ac4a225868bfa96feed133df075cb"},
+]
+
 [[package]]
 name = "gitdb"
 version = "4.0.10"
@@ -518,18 +582,21 @@ smmap = ">=3.0.1,<6"
 
 [[package]]
 name = "gitpython"
-version = "3.1.32"
+version = "3.1.36"
 description = "GitPython is a Python library used to interact with Git repositories"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "GitPython-3.1.32-py3-none-any.whl", hash = "sha256:e3d59b1c2c6ebb9dfa7a184daf3b6dd4914237e7488a1730a6d8f6f5d0b4187f"},
-    {file = "GitPython-3.1.32.tar.gz", hash = "sha256:8d9b8cb1e80b9735e8717c9362079d3ce4c6e5ddeebedd0361b228c3a67a62f6"},
+    {file = "GitPython-3.1.36-py3-none-any.whl", hash = "sha256:8d22b5cfefd17c79914226982bb7851d6ade47545b1735a9d010a2a4c26d8388"},
+    {file = "GitPython-3.1.36.tar.gz", hash = "sha256:4bb0c2a6995e85064140d31a33289aa5dce80133a23d36fcd372d716c54d3ebf"},
 ]
 
 [package.dependencies]
 gitdb = ">=4.0.1,<5"
 
+[package.extras]
+test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-sugar", "virtualenv"]
+
 [[package]]
 name = "graphlib-backport"
 version = "1.0.3"
@@ -630,13 +697,13 @@ pyreadline3 = {version = "*", markers = "sys_platform == \"win32\" and python_ve
 
 [[package]]
 name = "hypothesis"
-version = "6.82.6"
+version = "6.84.3"
 description = "A library for property-based testing"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "hypothesis-6.82.6-py3-none-any.whl", hash = "sha256:e99c445140e43f1cceda07b569f2f2d920d95435c6b0e6b507b35b01bb025e9d"},
-    {file = "hypothesis-6.82.6.tar.gz", hash = "sha256:f52ac4180a16208224e3d648fbf0fef8b9ca24863ba4b41bfef30a78c42646bd"},
+    {file = "hypothesis-6.84.3-py3-none-any.whl", hash = "sha256:4dd7de7a341a80c10d3e6beca12c084aab84c48ea270c1b9b8cee7e4aa5d7be2"},
+    {file = "hypothesis-6.84.3.tar.gz", hash = "sha256:b4117f4138e81986cf62ad4e1410a021adeaa52e4b0326419da626cd7d3b6250"},
 ]
 
 [package.dependencies]
@@ -662,13 +729,13 @@ zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2023.3)"]
 
 [[package]]
 name = "identify"
-version = "2.5.27"
+version = "2.5.28"
 description = "File identification library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "identify-2.5.27-py2.py3-none-any.whl", hash = "sha256:fdb527b2dfe24602809b2201e033c2a113d7bdf716db3ca8e3243f735dcecaba"},
-    {file = "identify-2.5.27.tar.gz", hash = "sha256:287b75b04a0e22d727bc9a41f0d4f3c1bcada97490fa6eabb5b28f0e9097e733"},
+    {file = "identify-2.5.28-py2.py3-none-any.whl", hash = "sha256:87816de144bf46d161bd5b3e8f5596b16cade3b80be537087334b26bc5c177f3"},
+    {file = "identify-2.5.28.tar.gz", hash = "sha256:94bb59643083ebd60dc996d043497479ee554381fbc5307763915cda49b0e78f"},
 ]
 
 [package.extras]
@@ -814,17 +881,18 @@ testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-chec
 
 [[package]]
 name = "jaraco-functools"
-version = "3.8.1"
+version = "3.9.0"
 description = "Functools like those found in stdlib"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jaraco.functools-3.8.1-py3-none-any.whl", hash = "sha256:784718fbc5d70c5a7bd881c362d23d561913102eb1381cec21327c8ebda3351c"},
-    {file = "jaraco.functools-3.8.1.tar.gz", hash = "sha256:e96a0d4ea455005a4092ce89a69ea0f7fb7e22807ad3b1008f9bf70c48d1cf2e"},
+    {file = "jaraco.functools-3.9.0-py3-none-any.whl", hash = "sha256:df2e2b0aadd2dfcee2d7e0d7d083d5a5b68f4c8621e6915ae9819a90de65dd44"},
+    {file = "jaraco.functools-3.9.0.tar.gz", hash = "sha256:8b137b0feacc17fef4bacee04c011c9e86f2341099c870a1d12d3be37b32a638"},
 ]
 
 [package.dependencies]
 more-itertools = "*"
+typing-extensions = {version = "*", markers = "python_version < \"3.11\""}
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
@@ -927,6 +995,24 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
+[[package]]
+name = "jinja2-ansible-filters"
+version = "1.3.2"
+description = "A port of Ansible's jinja2 filters without requiring ansible core."
+optional = false
+python-versions = "*"
+files = [
+    {file = "jinja2-ansible-filters-1.3.2.tar.gz", hash = "sha256:07c10cf44d7073f4f01102ca12d9a2dc31b41d47e4c61ed92ef6a6d2669b356b"},
+    {file = "jinja2_ansible_filters-1.3.2-py3-none-any.whl", hash = "sha256:e1082f5564917649c76fed239117820610516ec10f87735d0338688800a55b34"},
+]
+
+[package.dependencies]
+Jinja2 = "*"
+PyYAML = "*"
+
+[package.extras]
+test = ["pytest", "pytest-cov"]
+
 [[package]]
 name = "jsonschema"
 version = "4.19.0"
@@ -1479,28 +1565,47 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co
 
 [[package]]
 name = "pluggy"
-version = "1.2.0"
+version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pluggy-1.2.0-py3-none-any.whl", hash = "sha256:c2fd55a7d7a3863cba1a013e4e2414658b1d07b6bc57b3919e0c63c9abb99849"},
-    {file = "pluggy-1.2.0.tar.gz", hash = "sha256:d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3"},
+    {file = "pluggy-1.3.0-py3-none-any.whl", hash = "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"},
+    {file = "pluggy-1.3.0.tar.gz", hash = "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12"},
 ]
 
 [package.extras]
 dev = ["pre-commit", "tox"]
 testing = ["pytest", "pytest-benchmark"]
 
+[[package]]
+name = "plumbum"
+version = "1.8.2"
+description = "Plumbum: shell combinators library"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "plumbum-1.8.2-py3-none-any.whl", hash = "sha256:3ad9e5f56c6ec98f6f7988f7ea8b52159662ea9e915868d369dbccbfca0e367e"},
+    {file = "plumbum-1.8.2.tar.gz", hash = "sha256:9e6dc032f4af952665f32f3206567bc23b7858b1413611afe603a3f8ad9bfd75"},
+]
+
+[package.dependencies]
+pywin32 = {version = "*", markers = "platform_system == \"Windows\" and platform_python_implementation != \"PyPy\""}
+
+[package.extras]
+dev = ["paramiko", "psutil", "pytest (>=6.0)", "pytest-cov", "pytest-mock", "pytest-timeout"]
+docs = ["sphinx (>=4.0.0)", "sphinx-rtd-theme (>=1.0.0)"]
+ssh = ["paramiko"]
+
 [[package]]
 name = "poethepoet"
-version = "0.22.0"
+version = "0.22.1"
 description = "A task runner that works well with poetry."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "poethepoet-0.22.0-py3-none-any.whl", hash = "sha256:f654e52c19b7c689d5293ab6a065787b21f125884c0b367650292df4f3cb508c"},
-    {file = "poethepoet-0.22.0.tar.gz", hash = "sha256:659d7678fd8b349bd40941e3de7d6d386171dab3e7c8babcdcd8ead288c9ea47"},
+    {file = "poethepoet-0.22.1-py3-none-any.whl", hash = "sha256:1da4cd00d3b2c44b811c91616a744cf71094a26a299ea9956025162d34eef1a5"},
+    {file = "poethepoet-0.22.1.tar.gz", hash = "sha256:e758bcac731fa9ac0b812389589541e32b825c4a1894e16fa90aeb1946ba2823"},
 ]
 
 [package.dependencies]
@@ -1512,13 +1617,13 @@ poetry-plugin = ["poetry (>=1.0,<2.0)"]
 
 [[package]]
 name = "pre-commit"
-version = "3.3.3"
+version = "3.4.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pre_commit-3.3.3-py2.py3-none-any.whl", hash = "sha256:10badb65d6a38caff29703362271d7dca483d01da88f9d7e05d0b97171c136cb"},
-    {file = "pre_commit-3.3.3.tar.gz", hash = "sha256:a2256f489cd913d575c145132ae196fe335da32d91a8294b7afe6622335dd023"},
+    {file = "pre_commit-3.4.0-py2.py3-none-any.whl", hash = "sha256:96d529a951f8b677f730a7212442027e8ba53f9b04d217c4c67dc56c393ad945"},
+    {file = "pre_commit-3.4.0.tar.gz", hash = "sha256:6bbd5129a64cad4c0dfaeeb12cd8f7ea7e15b77028d985341478c8af3c759522"},
 ]
 
 [package.dependencies]
@@ -1528,6 +1633,20 @@ nodeenv = ">=0.11.1"
 pyyaml = ">=5.1"
 virtualenv = ">=20.10.0"
 
+[[package]]
+name = "prompt-toolkit"
+version = "3.0.36"
+description = "Library for building powerful interactive command lines in Python"
+optional = false
+python-versions = ">=3.6.2"
+files = [
+    {file = "prompt_toolkit-3.0.36-py3-none-any.whl", hash = "sha256:aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305"},
+    {file = "prompt_toolkit-3.0.36.tar.gz", hash = "sha256:3e163f254bef5a03b146397d7c1963bd3e2812f0964bb9a24e6ec761fd28db63"},
+]
+
+[package.dependencies]
+wcwidth = "*"
+
 [[package]]
 name = "psutil"
 version = "5.9.5"
@@ -1739,13 +1858,13 @@ files = [
 
 [[package]]
 name = "pyright"
-version = "1.1.324"
+version = "1.1.327"
 description = "Command line wrapper for pyright"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pyright-1.1.324-py3-none-any.whl", hash = "sha256:0edb712afbbad474e347de12ca1bd9368aa85d3365a1c7b795012e48e6a65111"},
-    {file = "pyright-1.1.324.tar.gz", hash = "sha256:0c48e3bca3d081bba0dddd0c1f075aaa965c59bba691f7b9bd9d73a98e44e0cf"},
+    {file = "pyright-1.1.327-py3-none-any.whl", hash = "sha256:3462cda239e9140276238bbdbd0b59d77406f1c2e14d8cb8c20c8e25639c6b3c"},
+    {file = "pyright-1.1.327.tar.gz", hash = "sha256:ba74148ad64f22020dbbed6781c4bdb38ecb8a7ca90dc3c87a4f08d1c0e11592"},
 ]
 
 [package.dependencies]
@@ -1757,13 +1876,13 @@ dev = ["twine (>=3.4.1)"]
 
 [[package]]
 name = "pytest"
-version = "7.4.0"
+version = "7.4.2"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pytest-7.4.0-py3-none-any.whl", hash = "sha256:78bf16451a2eb8c7a2ea98e32dc119fd2aa758f1d5d66dbf0a59d69a3969df32"},
-    {file = "pytest-7.4.0.tar.gz", hash = "sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a"},
+    {file = "pytest-7.4.2-py3-none-any.whl", hash = "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002"},
+    {file = "pytest-7.4.2.tar.gz", hash = "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"},
 ]
 
 [package.dependencies]
@@ -1847,13 +1966,13 @@ unidecode = ["Unidecode (>=1.1.1)"]
 
 [[package]]
 name = "pytz"
-version = "2023.3"
+version = "2023.3.post1"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
-    {file = "pytz-2023.3-py2.py3-none-any.whl", hash = "sha256:a151b3abb88eda1d4e34a9814df37de2a80e301e68ba0fd856fb9b46bfbbbffb"},
-    {file = "pytz-2023.3.tar.gz", hash = "sha256:1d8ce29db189191fb55338ee6d0387d82ab59f3d00eac103412d64e0ebd0c588"},
+    {file = "pytz-2023.3.post1-py2.py3-none-any.whl", hash = "sha256:ce42d816b81b68506614c11e8937d3aa9e41007ceb50bfdcb0749b921bf646c7"},
+    {file = "pytz-2023.3.post1.tar.gz", hash = "sha256:7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b"},
 ]
 
 [[package]]
@@ -1928,6 +2047,37 @@ files = [
     {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
 ]
 
+[[package]]
+name = "pyyaml-include"
+version = "1.3.1"
+description = "Extending PyYAML with a custom constructor for including YAML files within YAML files"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pyyaml-include-1.3.1.tar.gz", hash = "sha256:4cb3b4e1baae2ec251808fe1e8aed5d3d20699c541864c8e47ed866ab2f15039"},
+    {file = "pyyaml_include-1.3.1-py3-none-any.whl", hash = "sha256:e58525721a2938d29c4046350f8aad86f848660a770c29605e6f2700925fa753"},
+]
+
+[package.dependencies]
+PyYAML = ">=5.1,<7.0"
+
+[package.extras]
+toml = ["toml"]
+
+[[package]]
+name = "questionary"
+version = "2.0.1"
+description = "Python library to build pretty command line user prompts ⭐️"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "questionary-2.0.1-py3-none-any.whl", hash = "sha256:8ab9a01d0b91b68444dff7f6652c1e754105533f083cbe27597c8110ecc230a2"},
+    {file = "questionary-2.0.1.tar.gz", hash = "sha256:bcce898bf3dbb446ff62830c86c5c6fb9a22a54146f0f5597d3da43b10d8fc8b"},
+]
+
+[package.dependencies]
+prompt_toolkit = ">=2.0,<=3.0.36"
+
 [[package]]
 name = "referencing"
 version = "0.30.2"
@@ -1996,108 +2146,108 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
 [[package]]
 name = "rpds-py"
-version = "0.9.2"
+version = "0.10.3"
 description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
 python-versions = ">=3.8"
 files = [
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@@ -2208,19 +2358,19 @@ test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeo
 
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-    {file = "traitlets-5.9.0-py3-none-any.whl", hash = "sha256:9e6ec080259b9a5940c797d58b613b5e31441c2257b87c2e795c5228ae80d2d8"},
-    {file = "traitlets-5.9.0.tar.gz", hash = "sha256:f6cde21a9c68cf756af02035f72d5a723bf607e862e7be33ece505abf4a3bad9"},
+    {file = "traitlets-5.10.0-py3-none-any.whl", hash = "sha256:417745a96681fbb358e723d5346a547521f36e9bd0d50ba7ab368fff5d67aa54"},
+    {file = "traitlets-5.10.0.tar.gz", hash = "sha256:f584ea209240466e66e91f3c81aa7d004ba4cf794990b0c775938a1544217cd1"},
 ]
 
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
-test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"]
+test = ["argcomplete (>=3.0.3)", "mypy (>=1.5.1)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"]
 
 [[package]]
 name = "typing-extensions"
@@ -2671,13 +2821,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.24.3"
+version = "20.24.5"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.24.3-py3-none-any.whl", hash = "sha256:95a6e9398b4967fbcb5fef2acec5efaf9aa4972049d9ae41f95e0972a683fd02"},
-    {file = "virtualenv-20.24.3.tar.gz", hash = "sha256:e5c3b4ce817b0b328af041506a2a299418c98747c4b1e68cb7527e74ced23efc"},
+    {file = "virtualenv-20.24.5-py3-none-any.whl", hash = "sha256:b80039f280f4919c77b30f1c23294ae357c4c8701042086e3fc005963e4e537b"},
+    {file = "virtualenv-20.24.5.tar.gz", hash = "sha256:e8361967f6da6fbdf1426483bfe9fca8287c242ac0bc30429905721cefbff752"},
 ]
 
 [package.dependencies]
@@ -2686,9 +2836,20 @@ filelock = ">=3.12.2,<4"
 platformdirs = ">=3.9.1,<4"
 
 [package.extras]
-docs = ["furo (>=2023.5.20)", "proselint (>=0.13)", "sphinx (>=7.0.1)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
 test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
 
+[[package]]
+name = "wcwidth"
+version = "0.2.6"
+description = "Measures the displayed width of unicode strings in a terminal"
+optional = false
+python-versions = "*"
+files = [
+    {file = "wcwidth-0.2.6-py2.py3-none-any.whl", hash = "sha256:795b138f6875577cd91bba52baf9e445cd5118fd32723b460e30a0af30ea230e"},
+    {file = "wcwidth-0.2.6.tar.gz", hash = "sha256:a5220780a404dbe3353789870978e472cfe477761f06ee55077256e509b156d0"},
+]
+
 [[package]]
 name = "wrapt"
 version = "1.15.0"
@@ -2807,4 +2968,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.12"
-content-hash = "d6bc4ca4c26ff0f36a6535221686ef48b8a064e2f1077dfe1fba51232a1b3e99"
+content-hash = "2887048ebff450d3870d0beea93528797497aa5fc4e90791bb3b43180340a097"
diff --git a/pyproject.toml b/pyproject.toml
index 96f090b8..74364e16 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -64,6 +64,7 @@ scipy = [
     { version = ">=1.10.0,<=1.10.1", python = "<3.9" },
     { version = ">=1.10.0", python = ">=3.9" }
 ]
+copier = "^8.1.0"
 
 [tool.poetry.group.dev.dependencies]
 black = "^23.1.0"
diff --git a/snakebids/project_template/cookiecutter.json b/snakebids/project_template/cookiecutter.json
deleted file mode 100644
index f6bcb48d..00000000
--- a/snakebids/project_template/cookiecutter.json
+++ /dev/null
@@ -1,12 +0,0 @@
-{
-  "full_name": "",
-  "email": "",
-  "github": "",
-  "app_full_name": "Snakebids App",
-  "app_description": "",
-  "create_doc_template": ["False", "True"],
-  "_app_version": "0.1.0",
-  "_bids_version": "1.8.0",
-  "_snakebids_version": "0.0.0",
-  "__app_name": "{{ cookiecutter.app_full_name|lower|replace(' ', '_')|replace('-', '_') }}"
-}
diff --git a/snakebids/project_template/copier.yaml b/snakebids/project_template/copier.yaml
new file mode 100644
index 00000000..9d314da2
--- /dev/null
+++ b/snakebids/project_template/copier.yaml
@@ -0,0 +1,45 @@
+full_name:
+  type: str
+  help: What is your name?
+  placeholder: " optional"
+
+email:
+  type: str
+  help: What is your email?
+
+github:
+  type: str
+  help: What is your github username?
+
+app_full_name:
+  type: str
+  help: What is the name of your app?
+  default: "{{ dst_path }}"
+  validator: '{% if not app_full_name %}Required{% endif %}'
+
+app_description:
+  type: str
+  help: Provide a brief description of your app
+
+app_version:
+  default: "0.1.0"
+  help: Starting version number for your app
+
+create_doc_template:
+  type: bool
+  help: Would you to set up basic documentation?
+
+bids_version:
+  default: "1.8.0"
+  when: false
+
+snakebids_version:
+  default: "0.0.0"
+  when: false
+
+name_slug:
+  default: "{{ app_full_name|lower|replace(' ', '_')|replace('-', '_') }}"
+  when: false
+
+_jinja_extensions:
+  - jinja2_time.TimeExtension
diff --git a/snakebids/project_template/hooks/post_gen_project.py b/snakebids/project_template/hooks/post_gen_project.py
deleted file mode 100644
index 155c3896..00000000
--- a/snakebids/project_template/hooks/post_gen_project.py
+++ /dev/null
@@ -1,37 +0,0 @@
-from __future__ import annotations
-
-from importlib import metadata
-from shutil import rmtree
-
-
-def update_files(files: list[str] | str, replacement_str: str, cc_variable: str):
-    """Helper function to update cookiecutter content for certain files
-
-    INPUT
-    ------
-    files
-        file(s) to be updated
-    replacement_str
-        text to substitute into file(s)
-    cc_var
-        cookiecutter variable to replace (e.g.
-        {{ cookiecutter._snakebids_version }})
-    """
-    for fpath in files:
-        with open(fpath) as fcontent:
-            content = fcontent.read()
-
-        content = content.replace(cc_variable, replacement_str)
-
-        with open(fpath, "w", encoding="utf-8") as fcontent:
-            fcontent.write(content)
-
-
-# Replace snakebids version in cookiecutter
-sb_file_lists = ["setup.py", "docs/requirements.txt"]
-sb_version = metadata.version("snakebids")
-update_files(sb_file_lists, sb_version, "{{ cookiecutter._snakebids_version }}")
-
-# Remove documentation template
-if not {{cookiecutter.create_doc_template}}:  # noqa: F821
-    rmtree("docs")
diff --git a/snakebids/project_template/{{ name_slug }}/README.md.jinja b/snakebids/project_template/{{ name_slug }}/README.md.jinja
new file mode 100644
index 00000000..c4327223
--- /dev/null
+++ b/snakebids/project_template/{{ name_slug }}/README.md.jinja	
@@ -0,0 +1,3 @@
+# {{app_full_name}}
+
+{{ app_description }}
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/setup.py b/snakebids/project_template/{{ name_slug }}/setup.py.jinja
similarity index 88%
rename from snakebids/project_template/{{cookiecutter.__app_name}}/setup.py
rename to snakebids/project_template/{{ name_slug }}/setup.py.jinja
index d4a2e1ef..13ef84b7 100644
--- a/snakebids/project_template/{{cookiecutter.__app_name}}/setup.py
+++ b/snakebids/project_template/{{ name_slug }}/setup.py.jinja	
@@ -34,11 +34,11 @@
     ],
     entry_points={
         "console_scripts": [
-            "{{cookiecutter.__app_name}}={{cookiecutter.__app_name}}.run:main"
+            "{{name_slug}}={{name_slug}}.run:main"
         ]
     },
     install_requires=[
-        "snakebids>={{cookiecutter._snakebids_version}}",
+        "snakebids>={{snakebids_version}}",
         "snakemake",
     ],
     python_requires=">=3.7",
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/docs/.gitignore b/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/.gitignore
similarity index 100%
rename from snakebids/project_template/{{cookiecutter.__app_name}}/docs/.gitignore
rename to snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/.gitignore
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/docs/Makefile b/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/Makefile
similarity index 100%
rename from snakebids/project_template/{{cookiecutter.__app_name}}/docs/Makefile
rename to snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/Makefile
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/docs/conf.py b/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/conf.py.jinja
similarity index 92%
rename from snakebids/project_template/{{cookiecutter.__app_name}}/docs/conf.py
rename to snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/conf.py.jinja
index 869f0a12..ad690830 100644
--- a/snakebids/project_template/{{cookiecutter.__app_name}}/docs/conf.py
+++ b/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/conf.py.jinja	
@@ -17,9 +17,9 @@
 # -- Project information -----------------------------------------------------
 
 
-project = "{{cookiecutter.__app_name}}"
-copyright = "{% now 'utc', '%Y' %}, {{cookiecutter.full_name}}"
-author = "{{cookiecutter.full_name}}"
+project = "{{name_slug}}"
+copyright = "{% now 'utc', '%Y' %}, {{full_name}}"
+author = "{{full_name}}"
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/docs/getting_started/installation.md b/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/getting_started/installation.md.jinja
similarity index 71%
rename from snakebids/project_template/{{cookiecutter.__app_name}}/docs/getting_started/installation.md
rename to snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/getting_started/installation.md.jinja
index 56b38bfd..710cc7fe 100644
--- a/snakebids/project_template/{{cookiecutter.__app_name}}/docs/getting_started/installation.md
+++ b/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/getting_started/installation.md.jinja	
@@ -3,7 +3,7 @@
 Install from github with pip:
 
 ```bash
-pip install -e git+https://github.com/{{cookiecutter.github}}/{{cookiecutter.__app_name}}#egg={{cookiecutter.__app_name}}
+pip install -e git+https://github.com/{{github}}/{{name_slug}}#egg={{name_slug}}
 ```
 
 Note: you can re-run this command to re-install with the latest version
@@ -13,13 +13,13 @@ Note: you can re-run this command to re-install with the latest version
 Do a dry-run first (`-n`) and simply print (`-p`) what would be run:
 
 ```bash
-{{cookiecutter.__app_name}} /path/to/bids/dir /path/to/output/dir participant -np
+{{name_slug}} /path/to/bids/dir /path/to/output/dir participant -np
 ```
 
 Run the app, using all cores::
 
 ```bash
-{{cookiecutter.__app_name}} /path/to/bids/dir /path/to/output/dir participant --cores all
+{{name_slug}} /path/to/bids/dir /path/to/output/dir participant --cores all
 ```
 
 If any workflow rules require containers, then run with the `--use-singularity` option.
@@ -35,22 +35,22 @@ summarize outputs, by using the `report(...)` function on any snakemake output.
 To generate a report, run:
 
 ```bash
-{{cookiecutter.__app_name}} /path/to/bids/dir /path/to/output/dir participant --report
+{{name_slug}} /path/to/bids/dir /path/to/output/dir participant --report
 ```
 
 ## Compute Canada Instructions
 
 ### Setting up a dev environment
 
-Here are some instructions to get your python environment set-up on graham to run {{ cookiecutter.__app_name }}:
+Here are some instructions to get your python environment set-up on graham to run {{name_slug}}:
 
 # Create a virtualenv and activate it:
 
 ```bash
 cd $SCRATCH
 module load python/3
-virtualenv venv_{{ cookiecutter.__app_name }}
-source venv_{{ cookiecutter.__app_name }}/bin/activate
+virtualenv venv_{{name_slug}}
+source venv_{{name_slug}}/bin/activate
 ```
 
 # Follow the steps above to install from github repository
@@ -69,23 +69,23 @@ These are used in the instructions below.
 In an interactive job (for testing):
 
 ```bash
-regularInteractive -n 8 {{ cookiecutter.__app_name }} bids_dir out_dir participant --participant_label 001 -j 8
+regularInteractive -n 8 {{name_slug}} bids_dir out_dir participant --participant_label 001 -j 8
 ```
 
 Submitting a job (for larger cores, more subjects), still single job, but snakemake will parallelize over the 32 cores:
 
 ```bash
-regularSubmit -j Fat {{ cookiecutter.__app_name }} bids_dir out_dir participant  -j 32
+regularSubmit -j Fat {{name_slug}} bids_dir out_dir participant  -j 32
 ```
 
 Scaling up to ~hundred subjects (needs cc-slurm snakemake profile installed), submits 1 16core job per subject:
 
 ```bash
-{{ cookiecutter.__app_name }} bids_dir out_dir participant  --profile cc-slurm
+{{name_slug}} bids_dir out_dir participant  --profile cc-slurm
 ```
 
 Scaling up to even more subjects (uses group-components to bundle multiple subjects in each job), 1 32core job for N subjects (e.g. 10):
 
 ```bash
-{{ cookiecutter.__app_name }} bids_dir out_dir participant  --profile cc-slurm --group-components subj=10
-```
\ No newline at end of file
+{{name_slug}} bids_dir out_dir participant  --profile cc-slurm --group-components subj=10
+```
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/docs/index.md b/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/index.md
similarity index 100%
rename from snakebids/project_template/{{cookiecutter.__app_name}}/docs/index.md
rename to snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/index.md
diff --git a/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/requirements.txt.jinja b/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/requirements.txt.jinja
new file mode 100644
index 00000000..4af5df61
--- /dev/null
+++ b/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/requirements.txt.jinja	
@@ -0,0 +1,4 @@
+docutils<0.18
+sphinx-argparse
+sphinx_rtd_theme
+snakebids=={{ snakebids_version }}
diff --git a/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/usage/app_cli.md.jinja b/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/usage/app_cli.md.jinja
new file mode 100644
index 00000000..4d3625c1
--- /dev/null
+++ b/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/usage/app_cli.md.jinja	
@@ -0,0 +1,7 @@
+## Command line interface
+
+```{argparse}
+:filename: ../{{ name_slug }}/run.py
+:func: get_parser
+:prog: {{ name_slug }}
+```
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/docs/usage/snakemake_cli.md b/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md
similarity index 96%
rename from snakebids/project_template/{{cookiecutter.__app_name}}/docs/usage/snakemake_cli.md
rename to snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md
index d9b0f6b1..2e834372 100644
--- a/snakebids/project_template/{{cookiecutter.__app_name}}/docs/usage/snakemake_cli.md
+++ b/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md	
@@ -4,4 +4,4 @@
 :module: snakemake
 :func: get_argument_parser
 :prog: snakemake
-```
\ No newline at end of file
+```
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/{{cookiecutter.__app_name}}/config/snakebids.yml b/snakebids/project_template/{{ name_slug }}/{{name_slug}}/config/snakebids.yml
similarity index 99%
rename from snakebids/project_template/{{cookiecutter.__app_name}}/{{cookiecutter.__app_name}}/config/snakebids.yml
rename to snakebids/project_template/{{ name_slug }}/{{name_slug}}/config/snakebids.yml
index dd35a12d..9b36f37f 100644
--- a/snakebids/project_template/{{cookiecutter.__app_name}}/{{cookiecutter.__app_name}}/config/snakebids.yml
+++ b/snakebids/project_template/{{ name_slug }}/{{name_slug}}/config/snakebids.yml	
@@ -80,7 +80,7 @@ parse_args:
  # below are examples for plugin and custom parameters (e.g. config['smoothing_fwhm'])
   --skip_bids_validation:
     help: 'Skip validation of BIDS dataset. BIDS validation is performed by
-          default using the bids-validator plugin (if installed/enabled) or with the pybids 
+          default using the bids-validator plugin (if installed/enabled) or with the pybids
           validator implementation (if bids-validator is not installed/enabled).'
     dest: "plugins.validator.skip"
     action: "store_true"
diff --git a/snakebids/project_template/{{ name_slug }}/{{name_slug}}/pipeline_description.json.jinja b/snakebids/project_template/{{ name_slug }}/{{name_slug}}/pipeline_description.json.jinja
new file mode 100644
index 00000000..ec2c2953
--- /dev/null
+++ b/snakebids/project_template/{{ name_slug }}/{{name_slug}}/pipeline_description.json.jinja	
@@ -0,0 +1,22 @@
+{%
+    set generated = {
+        "Name":  name_slug,
+        "Version": app_version,
+    }
+-%}
+{%- if github -%}
+    {%- set _ = generated.update({"CodeURL": "https://github.com/" + github + "/" + name_slug}) -%}
+{%- endif -%}
+{%- if full_name -%}
+    {%- set _ = generated.update({"Author": full_name}) -%}
+{%- endif -%}
+{%- if email -%}
+    {%- set _ = generated.update({"AuthorEmail": email}) -%}
+{%- endif -%}
+{{- {
+        "Name": "Dataset generated by " + name_slug,
+        "BIDSVersion":  bids_version,
+        "DatasetType": "derivative",
+        "GeneratedBy": [generated],
+    } | to_json(indent=2)
+}}
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/{{cookiecutter.__app_name}}/run.py b/snakebids/project_template/{{ name_slug }}/{{name_slug}}/run.py.jinja
similarity index 88%
rename from snakebids/project_template/{{cookiecutter.__app_name}}/{{cookiecutter.__app_name}}/run.py
rename to snakebids/project_template/{{ name_slug }}/{{name_slug}}/run.py.jinja
index 80d4e2c8..f9426d23 100755
--- a/snakebids/project_template/{{cookiecutter.__app_name}}/{{cookiecutter.__app_name}}/run.py
+++ b/snakebids/project_template/{{ name_slug }}/{{name_slug}}/run.py.jinja	
@@ -7,7 +7,7 @@
 
 def get_parser():
     """Exposes parser for sphinx doc generation, cwd is the docs dir"""
-    app = SnakeBidsApp("../{{ cookiecutter.__app_name }}")
+    app = SnakeBidsApp("../{{ name_slug }}")
     return app.parser
 
 
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/{{cookiecutter.__app_name}}/workflow/Snakefile b/snakebids/project_template/{{ name_slug }}/{{name_slug}}/workflow/Snakefile
similarity index 100%
rename from snakebids/project_template/{{cookiecutter.__app_name}}/{{cookiecutter.__app_name}}/workflow/Snakefile
rename to snakebids/project_template/{{ name_slug }}/{{name_slug}}/workflow/Snakefile
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/README.md b/snakebids/project_template/{{cookiecutter.__app_name}}/README.md
deleted file mode 100644
index 84b5ca31..00000000
--- a/snakebids/project_template/{{cookiecutter.__app_name}}/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-# {{ cookiecutter.__app_name }}
-
-{{ cookiecutter.app_description }}
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/docs/requirements.txt b/snakebids/project_template/{{cookiecutter.__app_name}}/docs/requirements.txt
deleted file mode 100644
index 21901c99..00000000
--- a/snakebids/project_template/{{cookiecutter.__app_name}}/docs/requirements.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-docutils<0.18
-sphinx-argparse
-sphinx_rtd_theme
-snakebids=={{ cookiecutter._snakebids_version }}
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/docs/usage/app_cli.md b/snakebids/project_template/{{cookiecutter.__app_name}}/docs/usage/app_cli.md
deleted file mode 100644
index e5d49dfb..00000000
--- a/snakebids/project_template/{{cookiecutter.__app_name}}/docs/usage/app_cli.md
+++ /dev/null
@@ -1,7 +0,0 @@
-## Command line interface
-
-```{argparse}
-:filename: ../{{ cookiecutter.__app_name }}/run.py
-:func: get_parser
-:prog: {{ cookiecutter.__app_name }}
-```
\ No newline at end of file
diff --git a/snakebids/project_template/{{cookiecutter.__app_name}}/{{cookiecutter.__app_name}}/pipeline_description.json b/snakebids/project_template/{{cookiecutter.__app_name}}/{{cookiecutter.__app_name}}/pipeline_description.json
deleted file mode 100644
index e148f804..00000000
--- a/snakebids/project_template/{{cookiecutter.__app_name}}/{{cookiecutter.__app_name}}/pipeline_description.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
-    "Name": "Dataset generated by {{ cookiecutter.__app_name }}",
-    "BIDSVersion": "{{ cookiecutter._bids_version }}",
-    "DatasetType": "derivative",
-    "GeneratedBy": [
-        {
-            "Name": "{{ cookiecutter.__app_name }}",
-            "Version": "{{ cookiecutter._app_version }}"{%- if cookiecutter.github or cookiecutter.full_name or cookiecutter.email -%},{%- endif -%}
-            {% if cookiecutter.github %}
-            "CodeURL": "http://github.com/{{ cookiecutter.github }}/{{ cookiecutter.__app_name }}"{%- if cookiecutter.full_name or cookiecutter.email -%},{%- endif -%}
-            {%- endif -%}
-            {% if cookiecutter.full_name %}
-            "Author": "{{ cookiecutter.full_name }}"{%- if cookiecutter.email -%},{%- endif -%}
-            {%- endif -%}
-            {% if cookiecutter.email %}
-            "AuthorEmail": "{{ cookiecutter.email }}"{% endif %}
-        }
-    ]
-}