diff --git a/Cargo.lock b/Cargo.lock
index 6014dc67..f837bb6f 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -135,9 +135,9 @@ dependencies = [
 
 [[package]]
 name = "anyhow"
-version = "1.0.102"
+version = "1.0.104"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7f202df86484c868dbad7eaa557ef785d5c66295e41b460ef922eca0723b842c"
+checksum = "330a5ed07fa54e4702c9d6c4174f74427fc0ef6e214bbd677ae50a5099946470"
 
 [[package]]
 name = "approx"
@@ -1258,7 +1258,7 @@ version = "3.9.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "519bd3116aeeb42d5372c29d982d16d0170d3d4a5ed85fc7dd91642ffff3c67c"
 dependencies = [
- "darling 0.23.0",
+ "darling 0.20.11",
  "ident_case",
  "prettyplease",
  "proc-macro2",
@@ -1454,9 +1454,9 @@ dependencies = [
 
 [[package]]
 name = "chrono"
-version = "0.4.44"
+version = "0.4.45"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c673075a2e0e5f4a1dde27ce9dee1ea4558c7ffe648f576438a20ca1d2acc4b0"
+checksum = "1aa79e62e7697b8e29b513a68abacf485adcd1fe8284a4316c5ae868e6633327"
 dependencies = [
  "iana-time-zone",
  "js-sys",
@@ -1495,9 +1495,9 @@ dependencies = [
 
 [[package]]
 name = "clap"
-version = "4.6.1"
+version = "4.6.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1ddb117e43bbf7dacf0a4190fef4d345b9bad68dfc649cb349e7d17d28428e51"
+checksum = "dd059f9da4f5c36b3787f65d38ccaab1cc315f07b01f89abc8359ee6a8205011"
 dependencies = [
  "clap_builder",
  "clap_derive",
@@ -1505,9 +1505,9 @@ dependencies = [
 
 [[package]]
 name = "clap_builder"
-version = "4.6.0"
+version = "4.6.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "714a53001bf66416adb0e2ef5ac857140e7dc3a0c48fb28b2f10762fc4b5069f"
+checksum = "f09628afdcc538b57f3c6341e9c8e9970f18e4a481690a64974d7023bd33548b"
 dependencies = [
  "anstream",
  "anstyle",
@@ -1518,9 +1518,9 @@ dependencies = [
 
 [[package]]
 name = "clap_complete"
-version = "4.6.5"
+version = "4.6.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e0a7a9bfdb35811f9e59832f0f05975114d2251b415fb534108e6f34060fd772"
+checksum = "db8b397918185f0161ff3d6fcaa9e4bfc09b8367caf6e1d4a2848e5477ed027b"
 dependencies = [
  "clap",
 ]
@@ -1620,9 +1620,9 @@ dependencies = [
 
 [[package]]
 name = "commonwl"
-version = "0.8.1"
+version = "0.8.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "05508a26152f6006a6b5434dbdce81aec272875b1f27d829898b4e472db2bfce"
+checksum = "57bafe70af5c7fda6b0ad2ec7d40757fab2a864aa3b5d10be7671f9c72e55175"
 dependencies = [
  "cwl_core",
  "cwl_engine",
@@ -1647,16 +1647,16 @@ dependencies = [
  "pathdiff",
  "serde_core",
  "serde_json",
- "toml 1.1.2+spec-1.1.0",
+ "toml 1.1.3+spec-1.1.0",
  "winnow 1.0.3",
  "yaml-rust2",
 ]
 
 [[package]]
 name = "configparser"
-version = "3.1.0"
+version = "3.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e57e3272f0190c3f1584272d613719ba5fc7df7f4942fe542e63d949cf3a649b"
+checksum = "b46dec724fd22199ebde05033a0cbae453bc3b1ecff11eb6a6bb3eec4b90c6a4"
 
 [[package]]
 name = "console"
@@ -2193,7 +2193,7 @@ dependencies = [
  "miette",
  "regex",
  "serde",
- "serde-saphyr",
+ "serde-saphyr 0.0.27",
  "serde_json",
  "sha1 0.11.0",
  "thiserror 2.0.18",
@@ -2227,7 +2227,7 @@ dependencies = [
  "rdf",
  "semver 1.0.28",
  "serde",
- "serde-saphyr",
+ "serde-saphyr 0.0.27",
  "serde_json",
  "sha1 0.11.0",
  "sysinfo",
@@ -2271,7 +2271,7 @@ checksum = "a4caa74c460004ab32fe624b55191764a469fa12dbdaa0d2b6827d1dd2933d97"
 dependencies = [
  "cwl_salad_derive",
  "serde",
- "serde-saphyr",
+ "serde-saphyr 0.0.27",
  "serde_json",
 ]
 
@@ -2306,16 +2306,6 @@ dependencies = [
  "darling_macro 0.21.3",
 ]
 
-[[package]]
-name = "darling"
-version = "0.23.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "25ae13da2f202d56bd7f91c25fba009e7717a1e4a1cc98a76d844b65ae912e9d"
-dependencies = [
- "darling_core 0.23.0",
- "darling_macro 0.23.0",
-]
-
 [[package]]
 name = "darling_core"
 version = "0.20.11"
@@ -2343,19 +2333,6 @@ dependencies = [
  "syn 2.0.117",
 ]
 
-[[package]]
-name = "darling_core"
-version = "0.23.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9865a50f7c335f53564bb694ef660825eb8610e0a53d3e11bf1b0d3df31e03b0"
-dependencies = [
- "ident_case",
- "proc-macro2",
- "quote",
- "strsim",
- "syn 2.0.117",
-]
-
 [[package]]
 name = "darling_macro"
 version = "0.20.11"
@@ -2378,17 +2355,6 @@ dependencies = [
  "syn 2.0.117",
 ]
 
-[[package]]
-name = "darling_macro"
-version = "0.23.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ac3984ec7bd6cfa798e62b4a642426a5be0e68f9401cfc2a01e3fa9ea2fcdb8d"
-dependencies = [
- "darling_core 0.23.0",
- "quote",
- "syn 2.0.117",
-]
-
 [[package]]
 name = "dashmap"
 version = "6.2.1"
@@ -2556,7 +2522,7 @@ dependencies = [
 [[package]]
 name = "dioxus-attributes"
 version = "0.1.0"
-source = "git+https://github.com/DioxusLabs/components#837c9d4c1c9f99b19de7a3f087d8af1b0538dcae"
+source = "git+https://github.com/DioxusLabs/components#bf007c15d0cf4d04d3181cc46cf12325aa773955"
 dependencies = [
  "dioxus-rsx",
  "proc-macro2",
@@ -2943,7 +2909,7 @@ dependencies = [
 [[package]]
 name = "dioxus-primitives"
 version = "0.0.1"
-source = "git+https://github.com/DioxusLabs/components#837c9d4c1c9f99b19de7a3f087d8af1b0538dcae"
+source = "git+https://github.com/DioxusLabs/components#bf007c15d0cf4d04d3181cc46cf12325aa773955"
 dependencies = [
  "dioxus",
  "dioxus-attributes",
@@ -3701,9 +3667,9 @@ dependencies = [
 
 [[package]]
 name = "futures"
-version = "0.3.32"
+version = "0.3.33"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8b147ee9d1f6d097cef9ce628cd2ee62288d963e16fb287bd9286455b241382d"
+checksum = "a88cf1f829d945f548cf8fec32c61b1f202b6d93b45848602fc02af4b12ad218"
 dependencies = [
  "futures-channel",
  "futures-core",
@@ -3716,9 +3682,9 @@ dependencies = [
 
 [[package]]
 name = "futures-channel"
-version = "0.3.32"
+version = "0.3.33"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "07bbe89c50d7a535e539b8c17bc0b49bdb77747034daa8087407d655f3f7cc1d"
+checksum = "262590f4fe6afeb0bc83be1daa64e52657fe185690a958af7f3ad0e92085c5ae"
 dependencies = [
  "futures-core",
  "futures-sink",
@@ -3739,15 +3705,15 @@ dependencies = [
 
 [[package]]
 name = "futures-core"
-version = "0.3.32"
+version = "0.3.33"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7e3450815272ef58cec6d564423f6e755e25379b217b0bc688e295ba24df6b1d"
+checksum = "2cd50c473c80f6d7c3670a752354b8e569b1a7cbfdc0419ec88e5edad85e0dc7"
 
 [[package]]
 name = "futures-executor"
-version = "0.3.32"
+version = "0.3.33"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "baf29c38818342a3b26b5b923639e7b1f4a61fc5e76102d4b1981c6dc7a7579d"
+checksum = "6754879cc9f2c66f88c6e5c35344bb0bdb0708b0352b1201815667c7eabc7458"
 dependencies = [
  "futures-core",
  "futures-task",
@@ -3756,9 +3722,9 @@ dependencies = [
 
 [[package]]
 name = "futures-io"
-version = "0.3.32"
+version = "0.3.33"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cecba35d7ad927e23624b22ad55235f2239cfa44fd10428eecbeba6d6a717718"
+checksum = "4577ecaa3c4f96589d473f679a71b596316f6641bc350038b962a5daf0085d7a"
 
 [[package]]
 name = "futures-lite"
@@ -3775,9 +3741,9 @@ dependencies = [
 
 [[package]]
 name = "futures-macro"
-version = "0.3.32"
+version = "0.3.33"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e835b70203e41293343137df5c0664546da5745f82ec9b84d40be8336958447b"
+checksum = "2d6d3cde68c518367be28956066ddfef33813991b77a55005a69dae04bf3b10b"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -3786,15 +3752,15 @@ dependencies = [
 
 [[package]]
 name = "futures-sink"
-version = "0.3.32"
+version = "0.3.33"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c39754e157331b013978ec91992bde1ac089843443c49cbc7f46150b0fad0893"
+checksum = "e34418ac499d6305c2fb5ad0ed2f6ac998c5f8ca209b4510f7f94242c647e307"
 
 [[package]]
 name = "futures-task"
-version = "0.3.32"
+version = "0.3.33"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "037711b3d59c33004d3856fbdc83b99d4ff37a24768fa1be9ce3538a1cde4393"
+checksum = "b231ed28831efb4a61a08580c4bc233ec56bc009f4cd8f52da2c3cb97df0c109"
 
 [[package]]
 name = "futures-timer"
@@ -3804,9 +3770,9 @@ checksum = "af43fadb8a98512d547e37b4e92e0ced13e205c061b87b4623eff01d918d6968"
 
 [[package]]
 name = "futures-util"
-version = "0.3.32"
+version = "0.3.33"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "389ca41296e6190b48053de0321d02a77f32f8a5d2461dd38762c0593805c6d6"
+checksum = "a77a90a256fce34da66415271e30f94ee91c57b04b8a2c042d9cf3220179deaa"
 dependencies = [
  "futures-channel",
  "futures-core",
@@ -4231,6 +4197,16 @@ dependencies = [
  "smallvec",
 ]
 
+[[package]]
+name = "granit-parser"
+version = "0.0.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d03f81ad4732830d85cfd417a9f62cde6dadda4354d37d078a6084a19560aa2d"
+dependencies = [
+ "arraydeque",
+ "smallvec",
+]
+
 [[package]]
 name = "group"
 version = "0.13.0"
@@ -4722,7 +4698,7 @@ dependencies = [
  "libc",
  "percent-encoding",
  "pin-project-lite",
- "socket2 0.6.3",
+ "socket2 0.5.10",
  "system-configuration",
  "tokio",
  "tower-service",
@@ -4893,9 +4869,9 @@ dependencies = [
 
 [[package]]
 name = "ignore"
-version = "0.4.25"
+version = "0.4.30"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d3d782a365a015e0f5c04902246139249abf769125006fbe7649e2ee88169b4a"
+checksum = "7b009b6744c1445efd7244084e25e498636412effb6760b55067553baa925cc7"
 dependencies = [
  "crossbeam-deque",
  "globset",
@@ -5911,7 +5887,7 @@ version = "0.50.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7957b9740744892f114936ab4a57b3f487491bbeafaf8083688b16841a4240e5"
 dependencies = [
- "windows-sys 0.59.0",
+ "windows-sys 0.61.2",
 ]
 
 [[package]]
@@ -6890,7 +6866,7 @@ version = "3.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e67ba7e9b2b56446f1d419b1d807906278ffa1a658a8a5d8a39dcb1f5a78614f"
 dependencies = [
- "toml_edit 0.25.12+spec-1.1.0",
+ "toml_edit 0.25.13+spec-1.1.0",
 ]
 
 [[package]]
@@ -7062,7 +7038,7 @@ dependencies = [
  "quinn-udp",
  "rustc-hash 2.1.2",
  "rustls 0.23.40",
- "socket2 0.6.3",
+ "socket2 0.5.10",
  "thiserror 2.0.18",
  "tokio",
  "tracing",
@@ -7100,7 +7076,7 @@ dependencies = [
  "cfg_aliases",
  "libc",
  "once_cell",
- "socket2 0.6.3",
+ "socket2 0.5.10",
  "tracing",
  "windows-sys 0.60.2",
 ]
@@ -7163,9 +7139,9 @@ dependencies = [
 
 [[package]]
 name = "rand"
-version = "0.10.1"
+version = "0.10.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d2e8e8bcc7961af1fdac401278c6a831614941f6164ee3bf4ce61b7edb162207"
+checksum = "c7f5fa3a058cd35567ef9bfa5e75732bee0f9e4c55fa90477bef2dfcdbc4be80"
 dependencies = [
  "chacha20",
  "getrandom 0.4.2",
@@ -7360,7 +7336,7 @@ dependencies = [
  "serde_yaml",
  "tempfile",
  "tokio",
- "toml_edit 0.25.12+spec-1.1.0",
+ "toml_edit 0.25.13+spec-1.1.0",
  "util",
  "uuid",
 ]
@@ -7491,7 +7467,7 @@ dependencies = [
  "serde_yaml",
  "tempfile",
  "tokio",
- "toml 1.1.2+spec-1.1.0",
+ "toml 1.1.3+spec-1.1.0",
  "tracing",
  "util",
  "uuid",
@@ -7897,7 +7873,7 @@ dependencies = [
  "repository",
  "reqwest 0.13.4",
  "s4n_core",
- "serde-saphyr",
+ "serde-saphyr 0.0.29",
  "serde_json",
  "serial_test",
  "shlex 2.0.1",
@@ -7920,12 +7896,12 @@ dependencies = [
  "commonwl",
  "dunce",
  "pathdiff",
- "rand 0.10.1",
+ "rand 0.10.2",
  "repository",
  "rstest",
  "semver 1.0.28",
  "serde",
- "serde-saphyr",
+ "serde-saphyr 0.0.29",
  "serde_json",
  "serial_test",
  "shlex 2.0.1",
@@ -7935,8 +7911,8 @@ dependencies = [
  "test_utils",
  "tokio",
  "tokio-util",
- "toml 1.1.2+spec-1.1.0",
- "toml_edit 0.25.12+spec-1.1.0",
+ "toml 1.1.3+spec-1.1.0",
+ "toml_edit 0.25.13+spec-1.1.0",
  "util",
 ]
 
@@ -7949,15 +7925,6 @@ dependencies = [
  "winapi-util",
 ]
 
-[[package]]
-name = "scc"
-version = "2.4.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "46e6f046b7fef48e2660c57ed794263155d713de679057f2d0c169bfc6e756cc"
-dependencies = [
- "sdd",
-]
-
 [[package]]
 name = "schannel"
 version = "0.1.29"
@@ -8008,7 +7975,7 @@ dependencies = [
  "keyring",
  "pathdiff",
  "petgraph",
- "rand 0.10.1",
+ "rand 0.10.2",
  "reana",
  "remote_execution",
  "repository",
@@ -8024,7 +7991,7 @@ dependencies = [
  "tempfile",
  "tokio",
  "tokio-util",
- "toml 1.1.2+spec-1.1.0",
+ "toml 1.1.3+spec-1.1.0",
 ]
 
 [[package]]
@@ -8049,12 +8016,6 @@ dependencies = [
  "untrusted",
 ]
 
-[[package]]
-name = "sdd"
-version = "3.0.10"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "490dcfcbfef26be6800d11870ff2df8774fa6e86d047e3e8c8a76b25655e41ca"
-
 [[package]]
 name = "sec1"
 version = "0.7.3"
@@ -8178,7 +8139,7 @@ dependencies = [
  "base64",
  "encoding_rs_io",
  "getrandom 0.3.4",
- "granit-parser",
+ "granit-parser 0.0.3",
  "miette",
  "nohash-hasher",
  "num-traits",
@@ -8188,6 +8149,25 @@ dependencies = [
  "zmij",
 ]
 
+[[package]]
+name = "serde-saphyr"
+version = "0.0.29"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7bd22781911de0ca6debda95f073c8f18bec65d1a94f1fa9573f3102e514cea4"
+dependencies = [
+ "ahash",
+ "annotate-snippets",
+ "base64",
+ "encoding_rs_io",
+ "getrandom 0.3.4",
+ "granit-parser 0.0.7",
+ "nohash-hasher",
+ "num-traits",
+ "serde_core",
+ "smallvec",
+ "zmij",
+]
+
 [[package]]
 name = "serde-wasm-bindgen"
 version = "0.6.5"
@@ -8359,24 +8339,23 @@ dependencies = [
 
 [[package]]
 name = "serial_test"
-version = "3.4.0"
+version = "3.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "911bd979bf1070a3f3aa7b691a3b3e9968f339ceeec89e08c280a8a22207a32f"
+checksum = "699f4197115b8a7e7ff19c9a315a4bd6fffec26cc4626ef45ecaea389e081c6d"
 dependencies = [
  "futures-executor",
  "futures-util",
  "log",
  "once_cell",
  "parking_lot",
- "scc",
  "serial_test_derive",
 ]
 
 [[package]]
 name = "serial_test_derive"
-version = "3.4.0"
+version = "3.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0a7d91949b85b0d2fb687445e448b40d322b6b3e4af6b44a29b21d9a5f33e6d9"
+checksum = "94e153fc76e1c6a068703d6d29c508a0b15c061c4b7e43da59cc097bc342673c"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -9226,9 +9205,9 @@ checksum = "1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20"
 
 [[package]]
 name = "tokio"
-version = "1.52.3"
+version = "1.53.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8fc7f01b389ac15039e4dc9531aa973a135d7a4135281b12d7c1bc79fd57fffe"
+checksum = "d988bcd52dbe076d3d46903332f58c912b87a2c49b1428419a5845154762ffee"
 dependencies = [
  "bytes",
  "libc",
@@ -9346,9 +9325,9 @@ dependencies = [
 
 [[package]]
 name = "toml"
-version = "1.1.2+spec-1.1.0"
+version = "1.1.3+spec-1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "81f3d15e84cbcd896376e6730314d59fb5a87f31e4b038454184435cd57defee"
+checksum = "53c96ecdfa941c8fc4fcaed14f99ada8ebed502eef533015095a07e3301d4c3c"
 dependencies = [
  "indexmap 2.14.0",
  "serde_core",
@@ -9403,9 +9382,9 @@ dependencies = [
 
 [[package]]
 name = "toml_edit"
-version = "0.25.12+spec-1.1.0"
+version = "0.25.13+spec-1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d2153edc6955a6c354fad8f5efd38b6a8769bdccf9fe50f8e1329f81b0baa5d7"
+checksum = "6975367e4d2ef766d86af01ffad14b622fecc8d4357a998fbc4deb6e9bacaf9b"
 dependencies = [
  "indexmap 2.14.0",
  "serde_core",
@@ -9427,9 +9406,9 @@ dependencies = [
 
 [[package]]
 name = "toml_writer"
-version = "1.1.1+spec-1.1.0"
+version = "1.1.2+spec-1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "756daf9b1013ebe47a8776667b466417e2d4c5679d441c26230efd9ef78692db"
+checksum = "7d56353a2a665ad0f41a421187180aab746c8c325620617ad883a99a1cbe66d2"
 
 [[package]]
 name = "tower"
@@ -9763,9 +9742,9 @@ dependencies = [
 
 [[package]]
 name = "uuid"
-version = "1.23.1"
+version = "1.24.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ddd74a9687298c6858e9b88ec8935ec45d22e8fd5e6394fa1bd4e99a87789c76"
+checksum = "bf3923a6f5c4c6382e0b653c4117f48d631ea17f38ed86e2a828e6f7412f5239"
 dependencies = [
  "getrandom 0.4.2",
  "js-sys",
diff --git a/Cargo.toml b/Cargo.toml
index 3d7cef48..b6fceb16 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -41,7 +41,7 @@ keyring = { version = "3.6.3", features = [
 pathdiff = "0.2.3"
 serde = { version = "1.0.219", features = ["derive"] }
 serde_json = "1.0.149"
-serde-saphyr = "0.0.27"
+serde-saphyr = "0.0.29"
 serde_yaml = "0.9.34-deprecated"
 shlex = "2.0.1"
 rand = "0.10.1"