diff --git a/CHANGELOG.md b/CHANGELOG.md
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog for Shellify
 
+## 0.12.0
+- Add --allow-local-pinned-registries-to-be-prioritized switch
+- Prioiritise registries favouring those not pinned to local
+
 ## 0.11.0
 - Drop the shellify executable in favour or nix-shellify
 
diff --git a/shellify.cabal b/shellify.cabal
--- a/shellify.cabal
+++ b/shellify.cabal
@@ -1,6 +1,6 @@
 cabal-version:      3.0
 name:               shellify
-version:            0.11.0.5
+version:            0.12.0.0
 
 author: Daniel Rolls
 maintainer: daniel.rolls.27@googlemail.com
@@ -57,6 +57,7 @@
         extra >=1.7.13 && <1.9,
         HStringTemplate >=0.8.8 && <0.9,
         mtl >=2.2.2 && <2.4,
+        parsec >=3.1.17.0 && <3.2,
         shake >=0.19.7 && <0.20,
         unordered-containers >=0.2.19.1 && <0.3
 
@@ -75,6 +76,8 @@
     other-modules:
         Paths_shellify,
         TestHelpers
+    autogen-modules:
+        Paths_shellify
     ghc-options: -threaded -rtsopts -with-rtsopts=-N
     build-depends:
         hspec >=2.9.7 && <2.12,
diff --git a/src/Constants.hs b/src/Constants.hs
--- a/src/Constants.hs
+++ b/src/Constants.hs
@@ -26,6 +26,12 @@
     the versions of dependencies are kept for reproducibility and so that
     shells are cached to load faster.
 
+    --allow-local-pinned-registries-to-be-prioritized
+    Pinned local repoisitory URLs are usually taken last when looking for URLs for
+    generated flake.nix files. This is usually desired. If you do however want
+    to see these pinned entries in the flake file as specified in your registry,
+    then set this flag.
+
     --version
     Show the version number
 |]
diff --git a/src/Options.hs b/src/Options.hs
--- a/src/Options.hs
+++ b/src/Options.hs
@@ -29,6 +29,7 @@
     packages :: Packages
   , command :: Maybe Text
   , generateFlake :: Bool
+  , prioritiseLocalPinnedSystem :: Bool
 }
 
 data OptionsParser = OptionsParser [Text] -- remainingOptions
@@ -59,6 +60,7 @@
         oldStyleOption opt = baseOption opt
         newStyleOption "-p" = returnError "-p not supported with new style commands"
         newStyleOption "--packages" = returnError "--packages not supported with new style commands"
+        newStyleOption "--allow-local-pinned-registries-to-be-prioritized" = transformOptionsWith setPrioritiseLocalPinnedSystem
         newStyleOption arg | isSwitch arg = baseOption arg
                            | otherwise = transformOptionsWith $ appendPackages [arg]
         baseOption :: Text -> [Text] -> OptionsParser
@@ -82,6 +84,7 @@
         appendPackages ps opts = opts{packages=ps ++ packages opts}
         setCommand cmd opts = opts{command=Just cmd}
         setFlakeGeneration opts = opts{generateFlake=True}
+        setPrioritiseLocalPinnedSystem opts = opts {prioritiseLocalPinnedSystem=True}
         returnError errorText remaining = OptionsParser remaining $ Left errorText
 
 consumePackageArgs :: [Text] -> (Packages, [Text])
@@ -99,7 +102,7 @@
 isSwitch = isPrefixOf "-"
 
 instance Default Options where
-  def = Options [] Nothing False
+  def = Options [] Nothing False False
 
 instance Eq Options where
   a == b =  isEqual command
diff --git a/src/TemplateGeneration.hs b/src/TemplateGeneration.hs
--- a/src/TemplateGeneration.hs
+++ b/src/TemplateGeneration.hs
@@ -1,24 +1,23 @@
 module TemplateGeneration (generateShellDotNixText, generateFlakeText, getRegistryDB) where
 
-import Prelude hiding (lines)
-
 import Constants
 import FlakeTemplate
 import Options
 import ShellifyTemplate
 
+import Data.Bifunctor (bimap)
 import Data.Bool (bool)
-import Data.List (find, sort)
-import Data.List.Extra ((!?))
-import Data.Maybe (catMaybes, fromMaybe)
+import Data.List (find, sort, sortBy, sortOn)
+import Data.Maybe (fromMaybe)
 import Data.Set (fromList, toList)
-import Data.Text (isInfixOf, isPrefixOf, lines, pack, splitOn, Text())
+import Data.Text (Text(), isInfixOf, isPrefixOf, pack, splitOn, unpack)
 import Development.Shake.Command (cmd, Exit(Exit), Stderr(Stderr), Stdout(Stdout))
 import System.Exit (ExitCode (ExitSuccess))
+import Text.ParserCombinators.Parsec (Parser, char, endBy, eof, many1, noneOf, parse, string, (<|>))
 import Text.StringTemplate (newSTMP, render, setAttribute)
 
 generateFlakeText :: Text -> Options -> Maybe Text
-generateFlakeText db Options{packages=packages, generateFlake=shouldGenerateFlake} =
+generateFlakeText db Options{packages=packages, generateFlake=shouldGenerateFlake, prioritiseLocalPinnedSystem=prioritiseLocalPinnedSystem} =
   bool
     Nothing
     (Just $ render
@@ -28,15 +27,15 @@
           $ setAttribute "shell_args" shellArgs
           $ newSTMP flakeTemplate)
     shouldGenerateFlake
-  where repos = uniq $ getPackageRepo <$> sort packages
+  where repos = getPackageRepoWrapper packages
         repoVars = getPackageRepoVarName <$> repos
         repoInputs = repoInput <$> repos
         repoInputLine repoName url = repoName <> ".url = \"" <> url <> "\";"
         repoInput repoName = repoInputLine repoName .
           either
-            (error "Unexpected output from nix registry call: " <>)
+            (error . ("Unexpected output from nix registry call: " <>))
             (fromMaybe "PLEASE ENTER input here")
-            . findFlakeRepoUrl db $ repoName
+            . findFlakeRepoUrl prioritiseLocalPinnedSystem db $ repoName
         pkgsVar = (<> "Pkgs")
         pkgsVars = pkgsVar <$> repos
         pkgsDecls = (\repo -> pkgsDecl (pkgsVar repo) repo) <$> repos
@@ -52,9 +51,12 @@
           command
   $ newSTMP shellifyTemplate
   where pkgs = generateBuildInput <$> sort packages
-        parameters = uniq $ generateParameters <$> sort packages
+        parameters = generateParametersWrapper packages
         generateBuildInput input = (toImportVar . getPackageRepo) input <> "." <> getPackageName input
 
+getPackageRepoWrapper :: [Package] -> [Text]
+getPackageRepoWrapper = uniq . ("nixpkgs" :) . fmap getPackageRepo . sort
+
 getPackageRepo input | "#" `isInfixOf` input
                         = head $ splitOn "#" input
                      | otherwise
@@ -73,6 +75,9 @@
 getPackageRepoVarName "nixpkgs" = "pkgs"
 getPackageRepoVarName a = a
 
+generateParametersWrapper :: [Package] -> [Text]
+generateParametersWrapper = uniq . ("pkgs ? import <nixpkgs> {}" :) . fmap generateParameters . sort
+
 generateParameters :: Package -> Text
 generateParameters package | "#" `isInfixOf` package
                            && not ("nixpkgs#" `isPrefixOf` package)
@@ -90,23 +95,40 @@
                       (Right $ pack out)
                       (ex == ExitSuccess)
 
-findFlakeRepoUrl :: Text -> Text -> Either Text (Maybe Text)
-findFlakeRepoUrl haystack needle =
-       fmap repoUrl . find ((needle ==) . repoName) . catMaybes <$> mapM getFlakeRepo (lines haystack)
+findFlakeRepoUrl :: Bool -> Text -> Text -> Either String (Maybe Text)
+findFlakeRepoUrl prioritiseLocalPinnedSystem haystack needle =
+  bimap ((<>) "Error processing nix registry list output: " . show)
+        (fmap repoUrl . find ((needle ==) . repoName)
+                       . (if prioritiseLocalPinnedSystem then sortOn repoType else sortBy compareRepoEntries))
+        $ parse parseRepos "" . unpack $ haystack
 
+compareRepoEntries repoA repoB
+  | repoHasLocalPinning repoA && not (repoHasLocalPinning repoB) = GT
+  | repoHasLocalPinning repoB && not (repoHasLocalPinning repoA) = LT
+  | otherwise = repoType repoA `compare` repoType repoB
+  where repoHasLocalPinning = isPrefixOf "path:" . repoUrl
+
+data RepoType = User | System | Global
+                deriving (Eq, Ord)
+
 data FlakeRepo = FlakeRepo {
     repoName :: Text
   , repoUrl :: Text
+  , repoType :: RepoType
 }
 
-getFlakeRepo :: Text -> Either Text (Maybe FlakeRepo)
-getFlakeRepo line = let expectedField = maybe (Left "unexepected nix registry command format")
-                                              Right
-                                        . (!?) (splitOn " " line)
-                        urlField = expectedField 2
-                        splitRepoField = splitOn ":" <$> expectedField 1
-                        potentialFlakeName ["flake", b] = Just b
-                        potentialFlakeName _ = Nothing
-                        f x y = (`FlakeRepo` y) <$> potentialFlakeName x
-                     in f <$> splitRepoField <*> urlField
+parseRepos :: Parser [FlakeRepo]
+parseRepos = do res <- endBy parseLine (char '\n')
+                eof
+                return res
+  where parseLine = do repoType <- parseRepoType
+                       char ' '
+                       flakeName <- string "flake:" >> parseParam
+                       char ' '
+                       repoUrl <- parseParam
+                       return $ FlakeRepo (pack flakeName) (pack repoUrl) repoType
+        parseParam = many1 (noneOf " \n")
+        parseRepoType = (string "global" >> return Global)
+                    <|> (string "system" >> return System)
+                    <|> (string "user" >> return User)
 
diff --git a/test/Spec.hs b/test/Spec.hs
--- a/test/Spec.hs
+++ b/test/Spec.hs
@@ -1,4 +1,4 @@
-import Test.Hspec (describe, hspec, it, shouldBe)
+import Test.Hspec (describe, hspec, it, shouldBe, specify)
 
 import Options
 import TestHelpers
@@ -7,7 +7,8 @@
 main = hspec $ do
 
   describe "When passing option combinations" $ do
-    it "should print a message saying no package is specified when no argument is supplied" $
+
+    it "prints a message saying no package is specified when no argument is supplied" $
       shellifyWithArgs ""
         `shouldReturnSubstring`
       "without any packages specified"
@@ -17,12 +18,12 @@
         `shouldReturnSubstring`
       "without any packages specified"
 
-    it "should show help text when requested" $ do
+    it "shows help text when requested" $ do
       shellifyWithArgs "-h"
           `shouldReturnSubstring` "USAGE:"
       shellifyWithArgs "--help"
           `shouldReturnSubstring` "USAGE:"
-    it "should show the version number when requested" $ do
+    it "shows the version number when requested" $ do
       shellifyWithArgs "--version"
           `shouldReturnSubstring` "Shellify 0."
 
@@ -34,88 +35,145 @@
          `shouldBe`
         Left "--packages not supported with new style commands"
 
-    it "should allow a simple command to be specified with a package" $
-      theOptions "-p python --command cowsay"
-        `shouldBe`
-      Right def{packages=["python"], command=Just "cowsay"}
+    describe "When using the --command option" $ do
 
-    it "should allow a simple command to be specified before a package" $
-      theOptions "--run cowsay -p python"
-        `shouldBe`
-      Right def{packages=["python"], command=Just "cowsay"}
+      it "produces a shell with a shell hook" $
+          shellifyWithArgs "-p python -p cowsay --command cowsay"
+            `shouldReturnShellTextDefinedBy`
+          "two-build-inputs-and-command"
 
-    it "should allow a simple command to be specified before and after a package" $
-      theOptions "-p cowsay --command cowsay -p python"
-        `shouldBe`
-      Right def{packages=[ "cowsay", "python" ], command=Just "cowsay"}
+      it "allows a command to be specified with a package" $
+        theOptions "-p python --command cowsay"
+          `shouldBe`
+        Right def{packages=["python"], command=Just "cowsay"}
 
-    it "Should fail if command has no argument" $ do
-      shellifyWithArgs "--command -p python"
-          `shouldReturnSubstring` "Argument missing to switch"
-      shellifyWithArgs "--command"
-          `shouldReturnSubstring` "Argument missing to switch"
+      it "allows a command to be specified before a package" $
+        theOptions "--run cowsay -p python"
+          `shouldBe`
+        Right def{packages=["python"], command=Just "cowsay"}
 
-    it "should be able to specify one program to install after other arguments" $
+      it "allows a command to be specified before and after a package" $
+        theOptions "-p cowsay --command cowsay -p python"
+          `shouldBe`
+        Right def{packages=[ "cowsay", "python" ], command=Just "cowsay"}
+
+      it "fails if command has no argument" $ do
+        shellifyWithArgs "--command -p python"
+            `shouldReturnSubstring` "Argument missing to switch"
+        shellifyWithArgs "--command"
+            `shouldReturnSubstring` "Argument missing to switch"
+
+    it "supports specifying one program to install after other arguments" $
       "foo -p python"
         `shouldResultInPackages`
       [ "python" ]
 
-    it "should support multiple packages passed to -p" $
+    it "supports multiple packages passed to -p" $
       "-p python cowsay"
         `shouldResultInPackages`
       [ "cowsay", "python" ]
 
-    it "should only accept packages up to the next switch" $
+    it "only accepts packages up to the next switch" $
       "-p python --arg x 2"
         `shouldResultInPackages`
       [ "python" ]
 
-    it "should support multiple adjacent -p switches" $
+    it "supports multiple adjacent -p switches" $
       "-p python -p cowsay"
         `shouldResultInPackages`
       [ "python", "cowsay" ]
 
-    it "should support separated -p switches" $
+    it "supports separated -p switches" $
       "-p cowsay --foo -p python"
         `shouldResultInPackages`
       [ "cowsay", "python" ]
 
-    it "should support long switches" $
+    it "supports long switches" $
       "--packages cowsay"
         `shouldResultInPackages`
       [ "cowsay" ]
 
-    it "should support new shell commands" $
+    it "supports new shell commands" $
       theOptions "shell nixpkgs#python nixpkgs#cowsay"
         `shouldBe`
       Right def{packages=[ "nixpkgs#python", "nixpkgs#cowsay" ], generateFlake=True}
 
-  describe "when two buildInputs are required from two sources" $
-    shellifyWithArgs "--with-flake shell foo#cowsay nixpkgs#python"
-      `shouldReturnShellAndFlakeTextDefinedBy`
-    "inputs-from-know-and-unknown-sources"
+  describe "When dealing with multiple source repositories it should produce the correct output files for" $ do
 
-  describe "when using 2 simple buildInputs from one source" $
-    shellifyWithArgs "shell --with-flake python cowsay"
-      `shouldReturnShellAndFlakeTextDefinedBy`
-    "two-nixpkgs-inputs"
+    specify "one buildInput required from an unknown source" $
+      shellifyWithArgs "--with-flake shell foo#cowsay"
+        `shouldReturnShellAndFlakeTextDefinedBy`
+      "inputs-from-unknown-source"
 
-  describe "when pulling from 2 different known sources" $
-    shellifyWithArgs "shell nixpkgs#python blender-bin#blender_3_5"
-      `shouldReturnShellAndFlakeTextDefinedBy`
-    "inputs-from-different-registries"
+    specify "two buildInputs required from two sources" $
+      shellifyWithArgs "--with-flake shell foo#cowsay nixpkgs#python"
+        `shouldReturnShellAndFlakeTextDefinedBy`
+      "inputs-from-know-and-unknown-sources"
 
-  describe "when working with 2 nixkgs buildInputs" $
-      shellifyWithArgs "shell nixpkgs#python nixpkgs#cowsay"
-        `shouldReturnShellTextDefinedBy`
+    specify "2 buildInputs from one source" $
+      shellifyWithArgs "shell --with-flake python cowsay"
+        `shouldReturnShellAndFlakeTextDefinedBy`
       "two-nixpkgs-inputs"
 
-  describe "when working with multiple repos for known and unknown sources" $
-      shellifyWithArgs "shell nixpkgs#python foo#cowsay"
-        `shouldReturnShellTextDefinedBy`
-      "multiple-repository-sources"
+    specify "pulling from 2 different known sources" $
+      shellifyWithArgs "shell nixpkgs#python blender-bin#blender_3_5"
+        `shouldReturnShellAndFlakeTextDefinedBy`
+      "inputs-from-different-registries"
 
-  describe "when a command is specified" $
-      shellifyWithArgs "-p python -p cowsay --command cowsay"
-        `shouldReturnShellTextDefinedBy`
-      "two-build-inputs-and-command"
+    specify "2 nixpkgs buildInputs" $
+        shellifyWithArgs "shell nixpkgs#python nixpkgs#cowsay"
+          `shouldReturnShellTextDefinedBy`
+        "two-nixpkgs-inputs"
+
+    specify "multiple repos for known and unknown sources" $
+        shellifyWithArgs "shell nixpkgs#python foo#cowsay"
+          `shouldReturnShellTextDefinedBy`
+        "multiple-repository-sources"
+
+  describe "Where repository URLs need retrieving from the Nix Registry" $ do
+
+    it "falls through to global where system is local and global is available" $
+      whereALocalSystemAndFlakeGlobalNixpkgsExistsShellifyWithArgs "shell nixpkgs#cowsay"
+        `shouldReturnShellAndFlakeTextDefinedBy`
+      "cowsay-from-global-nixpkgs"
+
+    it "prefers system to global where system is local and always-take-from-system-registry is specified" $
+      whereALocalSystemAndFlakeGlobalNixpkgsExistsShellifyWithArgs "--allow-local-pinned-registries-to-be-prioritized shell nixpkgs#cowsay"
+        `shouldReturnShellAndFlakeTextDefinedBy`
+      "cowsay-from-local-nixpkgs"
+
+    it "uses the local url where system has a local URL and no user or global repository is available" $
+      whereALocalSystemNixpkgsExistsShellifyWithArgs "shell nixpkgs#cowsay"
+        `shouldReturnShellAndFlakeTextDefinedBy`
+      "cowsay-from-local-nixpkgs"
+
+    it "uses the user registry when no system or global alternative exists" $
+      whereAUserNixpkgsExistsShellifyWithArgs "shell nixpkgs#cowsay"
+        `shouldReturnShellAndFlakeTextDefinedBy`
+      "cowsay-from-user-nixpkgs"
+
+    it "uses the system custom registry when a system and then global alternative are defined" $
+      whereASystemAndGlobalCustomPkgsExistsShellifyWithArgs "shell custompkgs#cowsay"
+        `shouldReturnShellAndFlakeTextDefinedBy`
+      "cowsay-from-system-custompkgs"
+
+    it "uses the system custom registry when a global and then system alternative are defined" $
+      whereAGlobalAndSystemCustomPkgsExistsShellifyWithArgs "shell custompkgs#cowsay"
+        `shouldReturnShellAndFlakeTextDefinedBy`
+      "cowsay-from-system-custompkgs"
+
+    it "uses the system nixpkgs when a system and then global alternative exist" $
+      whereASystemAndGlobalNixpkgsExistsShellifyWithArgs "shell nixpkgs#cowsay"
+        `shouldReturnShellAndFlakeTextDefinedBy`
+      "cowsay-from-system-nixpkgs"
+
+    it "uses the system nixpkgs when a global and then system alternative exist" $
+      whereAGlobalAndSystemNixpkgsExistsShellifyWithArgs "shell nixpkgs#cowsay"
+        `shouldReturnShellAndFlakeTextDefinedBy`
+      "cowsay-from-system-nixpkgs"
+
+    it "uses the global nixpkgs when no alternative exists" $
+      whereOnlyAGlobalNixpkgsExistsShellifyWithArgs "shell nixpkgs#cowsay"
+        `shouldReturnShellAndFlakeTextDefinedBy`
+      "cowsay-from-global-nixpkgs"
+
diff --git a/test/TestHelpers.hs b/test/TestHelpers.hs
--- a/test/TestHelpers.hs
+++ b/test/TestHelpers.hs
@@ -1,11 +1,10 @@
 module TestHelpers where
 
-import Prelude hiding (last, putStrLn, readFile, reverse, tail, words)
+import Prelude hiding (last, putStrLn, readFile, reverse, tail, unlines, words)
 import Data.Bool (bool)
-import Data.Text (isInfixOf, last, reverse, tail, Text(), unpack, words)
+import Data.Text (isInfixOf, last, reverse, tail, Text(), unpack, unlines, words)
 import Data.Text.IO (putStrLn, readFile)
 import Test.Hspec (Expectation(), expectationFailure, it, shouldBe, shouldContain)
-
 import Options
 import Shellify
 import TemplateGeneration
@@ -17,17 +16,107 @@
       shellifyOutput
 
 shellifyWithArgs :: Text -> Either Text [(Text, Text)]
-shellifyWithArgs = parseOptionsAndCalculateExpectedFiles db "nix-shellify" . words
+shellifyWithArgs = shellifyWithArgsWithDb realDbExample
 
+realDbExample =
+  [ "global flake:agda github:agda/agda"
+  , "global flake:arion github:hercules-ci/arion"
+  , "global flake:blender-bin github:edolstra/nix-warez?dir=blender"
+  , "global flake:composable github:ComposableFi/composable"
+  , "global flake:dreampkgs github:nix-community/dreampkgs"
+  , "global flake:dwarffs github:edolstra/dwarffs"
+  , "global flake:emacs-overlay github:nix-community/emacs-overlay"
+  , "global flake:fenix github:nix-community/fenix"
+  , "global flake:flake-parts github:hercules-ci/flake-parts"
+  , "global flake:flake-utils github:numtide/flake-utils"
+  , "global flake:gemini github:nix-community/flake-gemini"
+  , "global flake:hercules-ci-effects github:hercules-ci/hercules-ci-effects"
+  , "global flake:hercules-ci-agent github:hercules-ci/hercules-ci-agent"
+  , "global flake:home-manager github:nix-community/home-manager"
+  , "global flake:hydra github:NixOS/hydra"
+  , "global flake:mach-nix github:DavHau/mach-nix"
+  , "global flake:nimble github:nix-community/flake-nimble"
+  , "global flake:nix github:NixOS/nix"
+  , "global flake:nix-darwin github:LnL7/nix-darwin"
+  , "global flake:nixops github:NixOS/nixops"
+  , "global flake:nixos-hardware github:NixOS/nixos-hardware"
+  , "global flake:nixos-homepage github:NixOS/nixos-homepage"
+  , "global flake:nixos-search github:NixOS/nixos-search"
+  , "global flake:nur github:nix-community/NUR"
+  , "global flake:nixpkgs github:NixOS/nixpkgs/nixpkgs-unstable"
+  , "global flake:templates github:NixOS/templates"
+  , "global flake:patchelf github:NixOS/patchelf"
+  , "global flake:poetry2nix github:nix-community/poetry2nix"
+  , "global flake:nix-serve github:edolstra/nix-serve"
+  , "global flake:nickel github:tweag/nickel"
+  , "global flake:bundlers github:NixOS/bundlers"
+  , "global flake:pridefetch github:SpyHoodle/pridefetch"
+  , "global flake:systems github:nix-systems/default"
+  , "global flake:helix github:helix-editor/helix"
+  , "global flake:sops-nix github:Mic92/sops-nix"
+  ]
+
+shellifyWithArgsWithDb :: [Text] -> Text -> Either Text [(Text, Text)]
+shellifyWithArgsWithDb customDb = parseOptionsAndCalculateExpectedFiles (unlines customDb) "nix-shellify" . words
+
+whereAUserNixpkgsExistsShellifyWithArgs :: Text -> Either Text [(Text, Text)]
+whereAUserNixpkgsExistsShellifyWithArgs = shellifyWithArgsWithDb
+  [ "global flake:nixpkgs github:NixOS/nixpkgs/nixpkgs-global-registry"
+  , "system flake:nixpkgs github:NixOS/nixpkgs/nixpkgs-system-registry"
+  , "user flake:nixpkgs github:NixOS/nixpkgs/nixpkgs-user-registry"
+  ]
+
+whereASystemAndGlobalCustomPkgsExistsShellifyWithArgs :: Text -> Either Text [(Text, Text)]
+whereASystemAndGlobalCustomPkgsExistsShellifyWithArgs = shellifyWithArgsWithDb
+  [ "global flake:custompkgs github:NixOS/custompkgs/custompkgs-global-registry"
+  , "system flake:custompkgs github:NixOS/custompkgs/custompkgs-system-registry"
+  , "global flake:nixpkgs github:NixOS/nixpkgs/nixpkgs-unstable"
+  ]
+
+whereAGlobalAndSystemCustomPkgsExistsShellifyWithArgs :: Text -> Either Text [(Text, Text)]
+whereAGlobalAndSystemCustomPkgsExistsShellifyWithArgs = shellifyWithArgsWithDb
+  [ "system flake:custompkgs github:NixOS/custompkgs/custompkgs-system-registry"
+  , "global flake:custompkgs github:NixOS/custompkgs/custompkgs-global-registry"
+  , "global flake:nixpkgs github:NixOS/nixpkgs/nixpkgs-unstable"
+  ]
+
+whereASystemAndGlobalNixpkgsExistsShellifyWithArgs :: Text -> Either Text [(Text, Text)]
+whereASystemAndGlobalNixpkgsExistsShellifyWithArgs = shellifyWithArgsWithDb
+  [ "system flake:nixpkgs github:NixOS/nixpkgs/nixpkgs-system-registry"
+  , "global flake:nixpkgs github:NixOS/nixpkgs/nixpkgs-global-registry"
+  ]
+
+whereAGlobalAndSystemNixpkgsExistsShellifyWithArgs :: Text -> Either Text [(Text, Text)]
+whereAGlobalAndSystemNixpkgsExistsShellifyWithArgs = shellifyWithArgsWithDb
+  [ "global flake:nixpkgs github:NixOS/nixpkgs/nixpkgs-global-registry"
+  , "system flake:nixpkgs github:NixOS/nixpkgs/nixpkgs-system-registry"
+  ]
+
+whereOnlyAGlobalNixpkgsExistsShellifyWithArgs :: Text -> Either Text [(Text, Text)]
+whereOnlyAGlobalNixpkgsExistsShellifyWithArgs = shellifyWithArgsWithDb
+  [ "global flake:nixpkgs github:NixOS/nixpkgs/nixpkgs-global-registry"
+  ]
+
+whereALocalSystemAndFlakeGlobalNixpkgsExistsShellifyWithArgs :: Text -> Either Text [(Text, Text)]
+whereALocalSystemAndFlakeGlobalNixpkgsExistsShellifyWithArgs = shellifyWithArgsWithDb
+  [ "system flake:nixpkgs path:/local/nixpkgs/path"
+  , "global flake:nixpkgs github:NixOS/nixpkgs/nixpkgs-global-registry"
+  ]
+
+whereALocalSystemNixpkgsExistsShellifyWithArgs :: Text -> Either Text [(Text, Text)]
+whereALocalSystemNixpkgsExistsShellifyWithArgs = shellifyWithArgsWithDb
+  [ "system flake:nixpkgs path:/local/nixpkgs/path"
+  , "global flake:templates github:NixOS/templates"
+  ]
+
+shouldReturnShellAndFlakeTextDefinedBy :: Either Text [(Text, Text)] -> FilePath -> Expectation
 shouldReturnShellAndFlakeTextDefinedBy result expectedOutput =
-     it "should produce the expected shell.nix and flake.nix" $
-       do expShell <- readNixTemplate (shellFile expectedOutput)
-          expFlake <- readNixTemplate (flakeFile expectedOutput)
-          result `shouldBe`
-              Right [("shell.nix", expShell),("flake.nix", expFlake)]
+   do expShell <- readNixTemplate (shellFile expectedOutput)
+      expFlake <- readNixTemplate (flakeFile expectedOutput)
+      result `shouldBe`
+          Right [("shell.nix", expShell),("flake.nix", expFlake)]
 
 shouldReturnShellTextDefinedBy result expectedOutput =
-     it "should produce the expected shell.nix" $
        do expShell <- readNixTemplate (shellFile expectedOutput)
           either
             (const $ expectationFailure "Expected Right but got Left")
@@ -36,14 +125,14 @@
                      fileName `shouldBe` "shell.nix")
             result
 
-theOptions = options "nix-shellify" . words
-
 shouldResultInPackages :: Text -> [Text] -> Expectation
 shouldResultInPackages parameters packages =
      theOptions parameters
        `shouldBe`
      Right def{packages=packages}
 
+theOptions = options "nix-shellify" . words
+
 instance Show Options
 
 readNixTemplate :: FilePath -> IO Text
@@ -56,4 +145,3 @@
 flakeFile = (<> "-flake.nix")
 shellFile = (<> "-shell.nix")
 
-db = "global flake:agda github:agda/agda\nglobal flake:arion github:hercules-ci/arion\nglobal flake:blender-bin github:edolstra/nix-warez?dir=blender\nglobal flake:composable github:ComposableFi/composable\nglobal flake:dreampkgs github:nix-community/dreampkgs\nglobal flake:dwarffs github:edolstra/dwarffs\nglobal flake:emacs-overlay github:nix-community/emacs-overlay\nglobal flake:fenix github:nix-community/fenix\nglobal flake:flake-parts github:hercules-ci/flake-parts\nglobal flake:flake-utils github:numtide/flake-utils\nglobal flake:gemini github:nix-community/flake-gemini\nglobal flake:hercules-ci-effects github:hercules-ci/hercules-ci-effects\nglobal flake:hercules-ci-agent github:hercules-ci/hercules-ci-agent\nglobal flake:home-manager github:nix-community/home-manager\nglobal flake:hydra github:NixOS/hydra\nglobal flake:mach-nix github:DavHau/mach-nix\nglobal flake:nimble github:nix-community/flake-nimble\nglobal flake:nix github:NixOS/nix\nglobal flake:nix-darwin github:LnL7/nix-darwin\nglobal flake:nixops github:NixOS/nixops\nglobal flake:nixos-hardware github:NixOS/nixos-hardware\nglobal flake:nixos-homepage github:NixOS/nixos-homepage\nglobal flake:nixos-search github:NixOS/nixos-search\nglobal flake:nur github:nix-community/NUR\nglobal flake:nixpkgs github:NixOS/nixpkgs/nixpkgs-unstable\nglobal flake:templates github:NixOS/templates\nglobal flake:patchelf github:NixOS/patchelf\nglobal flake:poetry2nix github:nix-community/poetry2nix\nglobal flake:nix-serve github:edolstra/nix-serve\nglobal flake:nickel github:tweag/nickel\nglobal flake:bundlers github:NixOS/bundlers\nglobal flake:pridefetch github:SpyHoodle/pridefetch\nglobal flake:systems github:nix-systems/default\nglobal flake:helix github:helix-editor/helix\nglobal flake:sops-nix github:Mic92/sops-nix\n" :: Text
diff --git a/test/outputs/cowsay-from-global-nixpkgs-flake.nix b/test/outputs/cowsay-from-global-nixpkgs-flake.nix
new file mode 100644
--- /dev/null
+++ b/test/outputs/cowsay-from-global-nixpkgs-flake.nix
@@ -0,0 +1,20 @@
+{
+  description = "my project description";
+
+  inputs = {
+
+    flake-utils.url = "github:numtide/flake-utils";
+    nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-global-registry";
+
+  };
+
+  outputs = { self, nixpkgs, flake-utils }:
+    flake-utils.lib.eachDefaultSystem
+      (system:
+        let nixpkgsPkgs = if builtins.hasAttr "packages" nixpkgs then nixpkgs.packages.${system} else ( if builtins.hasAttr "legacyPackages" nixpkgs then nixpkgs.legacyPackages.${system} else nixpkgs);
+        in
+        {
+          devShells.default = import ./shell.nix { pkgs=nixpkgsPkgs; };
+        }
+      );
+}
diff --git a/test/outputs/cowsay-from-global-nixpkgs-shell.nix b/test/outputs/cowsay-from-global-nixpkgs-shell.nix
new file mode 100644
--- /dev/null
+++ b/test/outputs/cowsay-from-global-nixpkgs-shell.nix
@@ -0,0 +1,9 @@
+{ pkgs ? import <nixpkgs> {} }:
+
+pkgs.mkShell {
+
+  buildInputs = [
+    pkgs.cowsay
+  ];
+
+}
diff --git a/test/outputs/cowsay-from-local-nixpkgs-flake.nix b/test/outputs/cowsay-from-local-nixpkgs-flake.nix
new file mode 100644
--- /dev/null
+++ b/test/outputs/cowsay-from-local-nixpkgs-flake.nix
@@ -0,0 +1,20 @@
+{
+  description = "my project description";
+
+  inputs = {
+
+    flake-utils.url = "github:numtide/flake-utils";
+    nixpkgs.url = "path:/local/nixpkgs/path";
+
+  };
+
+  outputs = { self, nixpkgs, flake-utils }:
+    flake-utils.lib.eachDefaultSystem
+      (system:
+        let nixpkgsPkgs = if builtins.hasAttr "packages" nixpkgs then nixpkgs.packages.${system} else ( if builtins.hasAttr "legacyPackages" nixpkgs then nixpkgs.legacyPackages.${system} else nixpkgs);
+        in
+        {
+          devShells.default = import ./shell.nix { pkgs=nixpkgsPkgs; };
+        }
+      );
+}
diff --git a/test/outputs/cowsay-from-local-nixpkgs-shell.nix b/test/outputs/cowsay-from-local-nixpkgs-shell.nix
new file mode 100644
--- /dev/null
+++ b/test/outputs/cowsay-from-local-nixpkgs-shell.nix
@@ -0,0 +1,9 @@
+{ pkgs ? import <nixpkgs> {} }:
+
+pkgs.mkShell {
+
+  buildInputs = [
+    pkgs.cowsay
+  ];
+
+}
diff --git a/test/outputs/cowsay-from-system-custompkgs-flake.nix b/test/outputs/cowsay-from-system-custompkgs-flake.nix
new file mode 100644
--- /dev/null
+++ b/test/outputs/cowsay-from-system-custompkgs-flake.nix
@@ -0,0 +1,22 @@
+{
+  description = "my project description";
+
+  inputs = {
+
+    flake-utils.url = "github:numtide/flake-utils";
+    custompkgs.url = "github:NixOS/custompkgs/custompkgs-system-registry";
+    nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-unstable";
+
+  };
+
+  outputs = { self, custompkgs, nixpkgs, flake-utils }:
+    flake-utils.lib.eachDefaultSystem
+      (system:
+        let custompkgsPkgs = if builtins.hasAttr "packages" custompkgs then custompkgs.packages.${system} else ( if builtins.hasAttr "legacyPackages" custompkgs then custompkgs.legacyPackages.${system} else custompkgs);
+            nixpkgsPkgs = if builtins.hasAttr "packages" nixpkgs then nixpkgs.packages.${system} else ( if builtins.hasAttr "legacyPackages" nixpkgs then nixpkgs.legacyPackages.${system} else nixpkgs);
+        in
+        {
+          devShells.default = import ./shell.nix { custompkgs=custompkgsPkgs; pkgs=nixpkgsPkgs; };
+        }
+      );
+}
diff --git a/test/outputs/cowsay-from-system-custompkgs-shell.nix b/test/outputs/cowsay-from-system-custompkgs-shell.nix
new file mode 100644
--- /dev/null
+++ b/test/outputs/cowsay-from-system-custompkgs-shell.nix
@@ -0,0 +1,9 @@
+{ custompkgs, pkgs ? import <nixpkgs> {} }:
+
+pkgs.mkShell {
+
+  buildInputs = [
+    custompkgs.cowsay
+  ];
+
+}
diff --git a/test/outputs/cowsay-from-system-nixpkgs-flake.nix b/test/outputs/cowsay-from-system-nixpkgs-flake.nix
new file mode 100644
--- /dev/null
+++ b/test/outputs/cowsay-from-system-nixpkgs-flake.nix
@@ -0,0 +1,20 @@
+{
+  description = "my project description";
+
+  inputs = {
+
+    flake-utils.url = "github:numtide/flake-utils";
+    nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-system-registry";
+
+  };
+
+  outputs = { self, nixpkgs, flake-utils }:
+    flake-utils.lib.eachDefaultSystem
+      (system:
+        let nixpkgsPkgs = if builtins.hasAttr "packages" nixpkgs then nixpkgs.packages.${system} else ( if builtins.hasAttr "legacyPackages" nixpkgs then nixpkgs.legacyPackages.${system} else nixpkgs);
+        in
+        {
+          devShells.default = import ./shell.nix { pkgs=nixpkgsPkgs; };
+        }
+      );
+}
diff --git a/test/outputs/cowsay-from-system-nixpkgs-shell.nix b/test/outputs/cowsay-from-system-nixpkgs-shell.nix
new file mode 100644
--- /dev/null
+++ b/test/outputs/cowsay-from-system-nixpkgs-shell.nix
@@ -0,0 +1,9 @@
+{ pkgs ? import <nixpkgs> {} }:
+
+pkgs.mkShell {
+
+  buildInputs = [
+    pkgs.cowsay
+  ];
+
+}
diff --git a/test/outputs/cowsay-from-user-nixpkgs-flake.nix b/test/outputs/cowsay-from-user-nixpkgs-flake.nix
new file mode 100644
--- /dev/null
+++ b/test/outputs/cowsay-from-user-nixpkgs-flake.nix
@@ -0,0 +1,20 @@
+{
+  description = "my project description";
+
+  inputs = {
+
+    flake-utils.url = "github:numtide/flake-utils";
+    nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-user-registry";
+
+  };
+
+  outputs = { self, nixpkgs, flake-utils }:
+    flake-utils.lib.eachDefaultSystem
+      (system:
+        let nixpkgsPkgs = if builtins.hasAttr "packages" nixpkgs then nixpkgs.packages.${system} else ( if builtins.hasAttr "legacyPackages" nixpkgs then nixpkgs.legacyPackages.${system} else nixpkgs);
+        in
+        {
+          devShells.default = import ./shell.nix { pkgs=nixpkgsPkgs; };
+        }
+      );
+}
diff --git a/test/outputs/cowsay-from-user-nixpkgs-shell.nix b/test/outputs/cowsay-from-user-nixpkgs-shell.nix
new file mode 100644
--- /dev/null
+++ b/test/outputs/cowsay-from-user-nixpkgs-shell.nix
@@ -0,0 +1,9 @@
+{ pkgs ? import <nixpkgs> {} }:
+
+pkgs.mkShell {
+
+  buildInputs = [
+    pkgs.cowsay
+  ];
+
+}
diff --git a/test/outputs/inputs-from-unknown-source-flake.nix b/test/outputs/inputs-from-unknown-source-flake.nix
new file mode 100644
--- /dev/null
+++ b/test/outputs/inputs-from-unknown-source-flake.nix
@@ -0,0 +1,22 @@
+{
+  description = "my project description";
+
+  inputs = {
+
+    flake-utils.url = "github:numtide/flake-utils";
+    foo.url = "PLEASE ENTER input here";
+    nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-unstable";
+
+  };
+
+  outputs = { self, foo, nixpkgs, flake-utils }:
+    flake-utils.lib.eachDefaultSystem
+      (system:
+        let fooPkgs = if builtins.hasAttr "packages" foo then foo.packages.${system} else ( if builtins.hasAttr "legacyPackages" foo then foo.legacyPackages.${system} else foo);
+            nixpkgsPkgs = if builtins.hasAttr "packages" nixpkgs then nixpkgs.packages.${system} else ( if builtins.hasAttr "legacyPackages" nixpkgs then nixpkgs.legacyPackages.${system} else nixpkgs);
+        in
+        {
+          devShells.default = import ./shell.nix { foo=fooPkgs; pkgs=nixpkgsPkgs; };
+        }
+      );
+}
diff --git a/test/outputs/inputs-from-unknown-source-shell.nix b/test/outputs/inputs-from-unknown-source-shell.nix
new file mode 100644
--- /dev/null
+++ b/test/outputs/inputs-from-unknown-source-shell.nix
@@ -0,0 +1,9 @@
+{ foo, pkgs ? import <nixpkgs> {} }:
+
+pkgs.mkShell {
+
+  buildInputs = [
+    foo.cowsay
+  ];
+
+}