diff --git a/Cargo.lock b/Cargo.lock
index 7630133..c84ff38 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -70,7 +70,7 @@ version = "1.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "5ca11d4be1bab0c8bc8734a9aa7bf4ee8316d462a08c6ac5052f888fef5b494b"
 dependencies = [
- "windows-sys",
+ "windows-sys 0.48.0",
 ]
 
 [[package]]
@@ -80,7 +80,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "58f54d10c6dfa51283a066ceab3ec1ab78d13fae00aa49243a45e4571fb79dfd"
 dependencies = [
  "anstyle",
- "windows-sys",
+ "windows-sys 0.48.0",
 ]
 
 [[package]]
@@ -233,7 +233,7 @@ checksum = "2674ec482fbc38012cf31e6c42ba0177b431a0cb6f15fe40efa5aab1bda516f6"
 dependencies = [
  "is-terminal",
  "lazy_static",
- "windows-sys",
+ "windows-sys 0.48.0",
 ]
 
 [[package]]
@@ -396,7 +396,7 @@ checksum = "136526188508e25c6fef639d7927dfb3e0e3084488bf202267829cf7fc23dbdd"
 dependencies = [
  "errno-dragonfly",
  "libc",
- "windows-sys",
+ "windows-sys 0.48.0",
 ]
 
 [[package]]
@@ -411,7 +411,7 @@ dependencies = [
 
 [[package]]
 name = "fasta_manipulation"
-version = "0.1.3"
+version = "0.1.4"
 dependencies = [
  "clap",
  "colored",
@@ -423,6 +423,7 @@ dependencies = [
  "serde",
  "serde_yaml",
  "stacker",
+ "walkdir",
 ]
 
 [[package]]
@@ -688,7 +689,7 @@ checksum = "cb0889898416213fab133e1d33a0e5858a48177452750691bde3666d0fdbaf8b"
 dependencies = [
  "hermit-abi",
  "rustix",
- "windows-sys",
+ "windows-sys 0.48.0",
 ]
 
 [[package]]
@@ -1099,7 +1100,7 @@ dependencies = [
  "errno",
  "libc",
  "linux-raw-sys",
- "windows-sys",
+ "windows-sys 0.48.0",
 ]
 
 [[package]]
@@ -1108,6 +1109,15 @@ version = "1.0.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1ad4cc8da4ef723ed60bced201181d83791ad433213d8c24efffda1eec85d741"
 
+[[package]]
+name = "same-file"
+version = "1.0.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502"
+dependencies = [
+ "winapi-util",
+]
+
 [[package]]
 name = "scale-info"
 version = "2.11.2"
@@ -1315,6 +1325,16 @@ version = "0.9.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f"
 
+[[package]]
+name = "walkdir"
+version = "2.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b"
+dependencies = [
+ "same-file",
+ "winapi-util",
+]
+
 [[package]]
 name = "winapi"
 version = "0.3.9"
@@ -1331,6 +1351,15 @@ version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
 
+[[package]]
+name = "winapi-util"
+version = "0.1.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b"
+dependencies = [
+ "windows-sys 0.52.0",
+]
+
 [[package]]
 name = "winapi-x86_64-pc-windows-gnu"
 version = "0.4.0"
@@ -1343,7 +1372,16 @@ version = "0.48.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9"
 dependencies = [
- "windows-targets",
+ "windows-targets 0.48.5",
+]
+
+[[package]]
+name = "windows-sys"
+version = "0.52.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d"
+dependencies = [
+ "windows-targets 0.52.6",
 ]
 
 [[package]]
@@ -1352,13 +1390,29 @@ version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c"
 dependencies = [
- "windows_aarch64_gnullvm",
- "windows_aarch64_msvc",
- "windows_i686_gnu",
- "windows_i686_msvc",
- "windows_x86_64_gnu",
- "windows_x86_64_gnullvm",
- "windows_x86_64_msvc",
+ "windows_aarch64_gnullvm 0.48.5",
+ "windows_aarch64_msvc 0.48.5",
+ "windows_i686_gnu 0.48.5",
+ "windows_i686_msvc 0.48.5",
+ "windows_x86_64_gnu 0.48.5",
+ "windows_x86_64_gnullvm 0.48.5",
+ "windows_x86_64_msvc 0.48.5",
+]
+
+[[package]]
+name = "windows-targets"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973"
+dependencies = [
+ "windows_aarch64_gnullvm 0.52.6",
+ "windows_aarch64_msvc 0.52.6",
+ "windows_i686_gnu 0.52.6",
+ "windows_i686_gnullvm",
+ "windows_i686_msvc 0.52.6",
+ "windows_x86_64_gnu 0.52.6",
+ "windows_x86_64_gnullvm 0.52.6",
+ "windows_x86_64_msvc 0.52.6",
 ]
 
 [[package]]
@@ -1367,42 +1421,90 @@ version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8"
 
+[[package]]
+name = "windows_aarch64_gnullvm"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3"
+
 [[package]]
 name = "windows_aarch64_msvc"
 version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc"
 
+[[package]]
+name = "windows_aarch64_msvc"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469"
+
 [[package]]
 name = "windows_i686_gnu"
 version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e"
 
+[[package]]
+name = "windows_i686_gnu"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b"
+
+[[package]]
+name = "windows_i686_gnullvm"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66"
+
 [[package]]
 name = "windows_i686_msvc"
 version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406"
 
+[[package]]
+name = "windows_i686_msvc"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66"
+
 [[package]]
 name = "windows_x86_64_gnu"
 version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e"
 
+[[package]]
+name = "windows_x86_64_gnu"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78"
+
 [[package]]
 name = "windows_x86_64_gnullvm"
 version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc"
 
+[[package]]
+name = "windows_x86_64_gnullvm"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d"
+
 [[package]]
 name = "windows_x86_64_msvc"
 version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538"
 
+[[package]]
+name = "windows_x86_64_msvc"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec"
+
 [[package]]
 name = "winnow"
 version = "0.5.40"
diff --git a/Cargo.toml b/Cargo.toml
index c2c2b73..1ef010b 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -16,3 +16,4 @@ regex = "1.9.5"
 serde = { version = "1.0.188", features = ["derive"] }
 serde_yaml = "0.9.25"
 stacker = "0.1.15"
+walkdir = "2.5.0"
diff --git a/README.md b/README.md
index 79c7001..1ea56bf 100644
--- a/README.md
+++ b/README.md
@@ -9,6 +9,12 @@ Currently, this program has the following arguments:
     This validates a given yaml against the TreeVal yaml standard. This is specific to the TreeVal pipeline.
     This command will go through the yaml and validate file and directory paths as well as files are in the expected format.
 
+    This has been tested by downloading the TreeValTinyTest data set:
+
+    ```bash
+    curl https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData.tar.gz | tar xzf -
+    ```
+
     `validateyaml ${PATH TO YAML} --verbose {DEFAULT FALSE} --output ${OUTPUT LOCATION OF LOGS}`
 
 -   map_headers