diff --git a/Arena.toml b/Arena.toml
index 2e159a0e..d76865b2 100644
--- a/Arena.toml
+++ b/Arena.toml
@@ -12,7 +12,7 @@ commit_hash = "ee08634f28810e5d6fd1a904fc83f4e67821550e"
 
 [repositories."stjudecloud/workflows"]
 identifier = "stjudecloud/workflows"
-commit_hash = "46a77b33c99c1952396fcaaf0845f1fb5a015987"
+commit_hash = "f67825369c2459e4b5a0ae970873e462af33d7b0"
 filters = ["/template/task-templates.wdl"]
 
 [[diagnostics]]
@@ -155,6 +155,11 @@ document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
 message = "ww-star-deseq2.wdl:125:6: warning[SnakeCase]: task name `ConcatenateFastQs` is not snake_case"
 permalink = "https://github.com/getwilds/ww-star-deseq2/blob/3de83fa91db1b2d1b0d91dfc20e3ca71303c8d15/ww-star-deseq2.wdl/#L125"
 
+[[diagnostics]]
+document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
+message = "ww-star-deseq2.wdl:126:3: warning[InputSorting]: input not sorted"
+permalink = "https://github.com/getwilds/ww-star-deseq2/blob/3de83fa91db1b2d1b0d91dfc20e3ca71303c8d15/ww-star-deseq2.wdl/#L126"
+
 [[diagnostics]]
 document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
 message = "ww-star-deseq2.wdl:133:15: warning[DoubleQuotes]: string defined with single quotes"
@@ -335,6 +340,11 @@ document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
 message = "ww-star-deseq2.wdl:79:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_SJ`"
 permalink = "https://github.com/getwilds/ww-star-deseq2/blob/3de83fa91db1b2d1b0d91dfc20e3ca71303c8d15/ww-star-deseq2.wdl/#L79"
 
+[[diagnostics]]
+document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
+message = "ww-star-deseq2.wdl:7:3: warning[InputSorting]: input not sorted"
+permalink = "https://github.com/getwilds/ww-star-deseq2/blob/3de83fa91db1b2d1b0d91dfc20e3ca71303c8d15/ww-star-deseq2.wdl/#L7"
+
 [[diagnostics]]
 document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
 message = "ww-star-deseq2.wdl:80:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_rnaseqc`"
@@ -370,6 +380,11 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:17:10: note[MissingMetas]: workflow `ww_vc_trio` is missing both meta and parameter_meta sections"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L17"
 
+[[diagnostics]]
+document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
+message = "ww-vc-trio.wdl:18:3: warning[InputSorting]: input not sorted"
+permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L18"
+
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:19:10: warning[SnakeCase]: input name `batchFile` is not snake_case"
@@ -480,6 +495,11 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:298:6: warning[SnakeCase]: task name `ApplyBaseRecalibrator` is not snake_case"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L298"
 
+[[diagnostics]]
+document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
+message = "ww-vc-trio.wdl:299:3: warning[InputSorting]: input not sorted"
+permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L299"
+
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:2:1: note[PreambleComments]: preamble comments cannot come after the version statement"
@@ -535,6 +555,11 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:353:6: warning[SnakeCase]: task name `bcftoolsMpileup` is not snake_case"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L353"
 
+[[diagnostics]]
+document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
+message = "ww-vc-trio.wdl:354:3: warning[InputSorting]: input not sorted"
+permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L354"
+
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:35:10: warning[SnakeCase]: input name `dbSNP_vcf_index` is not snake_case"
@@ -580,6 +605,11 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:420:6: warning[SnakeCase]: task name `BwaMem` is not snake_case"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L420"
 
+[[diagnostics]]
+document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
+message = "ww-vc-trio.wdl:421:3: warning[InputSorting]: input not sorted"
+permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L421"
+
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:441:1: note[LineWidth]: line exceeds maximum width of 90"
@@ -595,6 +625,11 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:456:6: warning[SnakeCase]: task name `CollectHsMetrics` is not snake_case"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L456"
 
+[[diagnostics]]
+document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
+message = "ww-vc-trio.wdl:457:3: warning[InputSorting]: input not sorted"
+permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L457"
+
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:45:17: warning[SnakeCase]: private declaration name `batchInfo` is not snake_case"
@@ -685,6 +720,11 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:518:6: warning[SnakeCase]: task name `HaplotypeCaller` is not snake_case"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L518"
 
+[[diagnostics]]
+document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
+message = "ww-vc-trio.wdl:519:3: warning[InputSorting]: input not sorted"
+permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L519"
+
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:51:10: warning[SnakeCase]: private declaration name `annovarDocker` is not snake_case"
@@ -720,6 +760,11 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:558:6: warning[SnakeCase]: task name `MergeBamAlignment` is not snake_case"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L558"
 
+[[diagnostics]]
+document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
+message = "ww-vc-trio.wdl:559:3: warning[InputSorting]: input not sorted"
+permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L559"
+
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:571:1: note[LineWidth]: line exceeds maximum width of 90"
@@ -735,6 +780,11 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:596:6: warning[SnakeCase]: task name `Mutect2TumorOnly` is not snake_case"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L596"
 
+[[diagnostics]]
+document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
+message = "ww-vc-trio.wdl:597:3: warning[InputSorting]: input not sorted"
+permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a904fc83f4e67821550e/ww-vc-trio.wdl/#L597"
+
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:605:10: warning[SnakeCase]: input name `genomeReference` is not snake_case"
@@ -838,644 +888,639 @@ permalink = "https://github.com/getwilds/ww-vc-trio/blob/ee08634f28810e5d6fd1a90
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:129:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L129"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L129"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:12:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L12"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L12"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:13:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L13"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L13"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:14:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L14"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L14"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:173:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L173"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L173"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:182:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L182"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L182"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:206:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L206"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L206"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:2:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L2"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L2"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:32:12: warning[SnakeCase]: struct member name `ID` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L32"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L32"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:33:13: warning[SnakeCase]: struct member name `BC` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L33"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L33"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:34:13: warning[SnakeCase]: struct member name `CN` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L34"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L34"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:35:13: warning[SnakeCase]: struct member name `DS` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L35"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L35"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:36:13: warning[SnakeCase]: struct member name `DT` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L36"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L36"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:37:13: warning[SnakeCase]: struct member name `FO` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L37"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L37"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:38:13: warning[SnakeCase]: struct member name `KS` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L38"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L38"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:39:13: warning[SnakeCase]: struct member name `LB` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L39"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L39"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:3:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L3"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L3"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:40:13: warning[SnakeCase]: struct member name `PG` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L40"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L40"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:41:10: warning[SnakeCase]: struct member name `PI` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L41"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L41"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:42:13: warning[SnakeCase]: struct member name `PL` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L42"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L42"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:43:13: warning[SnakeCase]: struct member name `PM` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L43"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L43"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:44:13: warning[SnakeCase]: struct member name `PU` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L44"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L44"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:45:13: warning[SnakeCase]: struct member name `SM` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/data_structures/read_group.wdl/#L45"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/data_structures/read_group.wdl/#L45"
 
 [[diagnostics]]
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-
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 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl"
-message = "rnaseq-variant-calling.wdl:43:14: warning[SnakeCase]: input name `dbSNP_vcf_index` is not snake_case"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/rnaseq/rnaseq-variant-calling.wdl/#L43"
+message = "rnaseq-variant-calling.wdl:40:14: warning[SnakeCase]: input name `dbSNP_vcf` is not snake_case"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/rnaseq/rnaseq-variant-calling.wdl/#L40"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl"
-message = "rnaseq-variant-calling.wdl:4:1: note[ImportSort]: imports are not sorted lexicographically"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/rnaseq/rnaseq-variant-calling.wdl/#L4"
+message = "rnaseq-variant-calling.wdl:41:14: warning[SnakeCase]: input name `dbSNP_vcf_index` is not snake_case"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/rnaseq/rnaseq-variant-calling.wdl/#L41"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
 message = "10x-bam-to-fastqs.wdl:28:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L28"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L28"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
 message = "10x-bam-to-fastqs.wdl:29:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L29"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L29"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
 message = "10x-bam-to-fastqs.wdl:32:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L32"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L32"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
 message = "10x-bam-to-fastqs.wdl:35:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L35"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L35"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
 message = "10x-bam-to-fastqs.wdl:36:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L36"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L36"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
 message = "10x-bam-to-fastqs.wdl:37:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L37"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L37"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
 message = "10x-bam-to-fastqs.wdl:38:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L38"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L38"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
 message = "10x-bam-to-fastqs.wdl:47:10: note[MissingMetas]: workflow `cell_ranger_bam_to_fastqs` is missing a `meta` section"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L47"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L47"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
 message = "10x-bam-to-fastqs.wdl:87:6: note[MissingMetas]: task `parse_input` is missing a `meta` section"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L87"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L87"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/scrnaseq-standard.wdl"
 message = "scrnaseq-standard.wdl:18:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/scrnaseq-standard.wdl/#L18"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/scrnaseq-standard.wdl/#L18"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/scrnaseq-standard.wdl"
 message = "scrnaseq-standard.wdl:19:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/scrnaseq-standard.wdl/#L19"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/scrnaseq-standard.wdl/#L19"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/scrnaseq-standard.wdl"
 message = "scrnaseq-standard.wdl:22:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/scrnaseq-standard.wdl/#L22"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/scrnaseq-standard.wdl/#L22"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/scrnaseq-standard.wdl"
 message = "scrnaseq-standard.wdl:25:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/scrnaseq-standard.wdl/#L25"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/scrnaseq-standard.wdl/#L25"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/scrnaseq-standard.wdl"
 message = "scrnaseq-standard.wdl:26:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/scrnaseq-standard.wdl/#L26"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/scrnaseq-standard.wdl/#L26"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/scrnaseq-standard.wdl"
 message = "scrnaseq-standard.wdl:27:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/scrnaseq-standard.wdl/#L27"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/scrnaseq-standard.wdl/#L27"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/scrnaseq-standard.wdl"
 message = "scrnaseq-standard.wdl:28:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/scrnaseq-standard.wdl/#L28"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/scrnaseq-standard.wdl/#L28"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/scrnaseq-standard.wdl"
 message = "scrnaseq-standard.wdl:40:10: note[MissingMetas]: workflow `scrnaseq_standard` is missing a `meta` section"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/scrnaseq-standard.wdl/#L40"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/scrnaseq-standard.wdl/#L40"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/scrnaseq/scrnaseq-standard.wdl"
 message = "scrnaseq-standard.wdl:5:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/46a77b33c99c1952396fcaaf0845f1fb5a015987/workflows/scrnaseq/scrnaseq-standard.wdl/#L5"
+permalink = "https://github.com/stjudecloud/workflows/blob/f67825369c2459e4b5a0ae970873e462af33d7b0/workflows/scrnaseq/scrnaseq-standard.wdl/#L5"
diff --git a/Gauntlet.toml b/Gauntlet.toml
index 76468efb..e6c07f61 100644
--- a/Gauntlet.toml
+++ b/Gauntlet.toml
@@ -44,7 +44,7 @@ commit_hash = "ee08634f28810e5d6fd1a904fc83f4e67821550e"
 
 [repositories."stjudecloud/workflows"]
 identifier = "stjudecloud/workflows"
-commit_hash = "46a77b33c99c1952396fcaaf0845f1fb5a015987"
+commit_hash = "f67825369c2459e4b5a0ae970873e462af33d7b0"
 filters = ["/template/task-templates.wdl"]
 
 [repositories."theiagen/public_health_bioinformatics"]
diff --git a/wdl-ast/src/v1/decls.rs b/wdl-ast/src/v1/decls.rs
index 922a0fee..135516ed 100644
--- a/wdl-ast/src/v1/decls.rs
+++ b/wdl-ast/src/v1/decls.rs
@@ -74,6 +74,18 @@ impl fmt::Display for MapType {
     }
 }
 
+impl PartialOrd for MapType {
+    fn partial_cmp(&self, other: &Self) -> Option<std::cmp::Ordering> {
+        Some(self.cmp(other))
+    }
+}
+
+impl Ord for MapType {
+    fn cmp(&self, other: &Self) -> std::cmp::Ordering {
+        self.types().cmp(&other.types())
+    }
+}
+
 /// Represents an `Array` type.
 #[derive(Clone, Debug, PartialEq, Eq)]
 pub struct ArrayType(SyntaxNode);
@@ -135,6 +147,24 @@ impl fmt::Display for ArrayType {
     }
 }
 
+impl PartialOrd for ArrayType {
+    fn partial_cmp(&self, other: &Self) -> Option<std::cmp::Ordering> {
+        Some(self.cmp(other))
+    }
+}
+
+impl Ord for ArrayType {
+    fn cmp(&self, other: &Self) -> std::cmp::Ordering {
+        if self.is_non_empty() && !other.is_non_empty() {
+            std::cmp::Ordering::Less
+        } else if !self.is_non_empty() && other.is_non_empty() {
+            std::cmp::Ordering::Greater
+        } else {
+            self.element_type().cmp(&other.element_type())
+        }
+    }
+}
+
 /// Represents a `Pair` type.
 #[derive(Clone, Debug, PartialEq, Eq)]
 pub struct PairType(SyntaxNode);
@@ -193,6 +223,18 @@ impl fmt::Display for PairType {
     }
 }
 
+impl PartialOrd for PairType {
+    fn partial_cmp(&self, other: &Self) -> Option<std::cmp::Ordering> {
+        Some(self.cmp(other))
+    }
+}
+
+impl Ord for PairType {
+    fn cmp(&self, other: &Self) -> std::cmp::Ordering {
+        self.types().cmp(&other.types())
+    }
+}
+
 /// Represents a `Object` type.
 #[derive(Clone, Debug, PartialEq, Eq)]
 pub struct ObjectType(SyntaxNode);
@@ -242,6 +284,18 @@ impl fmt::Display for ObjectType {
     }
 }
 
+impl PartialOrd for ObjectType {
+    fn partial_cmp(&self, other: &Self) -> Option<std::cmp::Ordering> {
+        Some(self.cmp(other))
+    }
+}
+
+impl Ord for ObjectType {
+    fn cmp(&self, _: &Self) -> std::cmp::Ordering {
+        std::cmp::Ordering::Equal
+    }
+}
+
 /// Represents a reference to a type.
 #[derive(Clone, Debug, PartialEq, Eq)]
 pub struct TypeRef(SyntaxNode);
@@ -297,6 +351,18 @@ impl fmt::Display for TypeRef {
     }
 }
 
+impl PartialOrd for TypeRef {
+    fn partial_cmp(&self, other: &Self) -> Option<std::cmp::Ordering> {
+        Some(self.cmp(other))
+    }
+}
+
+impl Ord for TypeRef {
+    fn cmp(&self, _: &Self) -> std::cmp::Ordering {
+        std::cmp::Ordering::Equal
+    }
+}
+
 /// Represents a kind of primitive type.
 #[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
 pub enum PrimitiveTypeKind {
@@ -339,6 +405,17 @@ impl PrimitiveType {
             Some(SyntaxKind::QuestionMark)
         )
     }
+
+    /// Defines an ordering for PrimitiveTypes
+    fn primitive_type_index(&self) -> usize {
+        match self.kind() {
+            PrimitiveTypeKind::Boolean => 2,
+            PrimitiveTypeKind::Integer => 4,
+            PrimitiveTypeKind::Float => 3,
+            PrimitiveTypeKind::String => 1,
+            PrimitiveTypeKind::File => 0,
+        }
+    }
 }
 
 impl AstNode for PrimitiveType {
@@ -384,6 +461,19 @@ impl fmt::Display for PrimitiveType {
     }
 }
 
+impl PartialOrd for PrimitiveType {
+    fn partial_cmp(&self, other: &Self) -> Option<std::cmp::Ordering> {
+        Some(self.cmp(other))
+    }
+}
+
+impl Ord for PrimitiveType {
+    fn cmp(&self, other: &Self) -> std::cmp::Ordering {
+        self.primitive_type_index()
+            .cmp(&other.primitive_type_index())
+    }
+}
+
 /// Represents a type.
 #[derive(Clone, Debug, PartialEq, Eq)]
 pub enum Type {
@@ -455,7 +545,7 @@ impl Type {
     /// # Panics
     ///
     /// Panics if the type is not an object type.
-    pub fn unwrap_objet_type(self) -> ObjectType {
+    pub fn unwrap_object_type(self) -> ObjectType {
         match self {
             Self::Object(ty) => ty,
             _ => panic!("not an object type"),
@@ -485,6 +575,27 @@ impl Type {
             _ => panic!("not a primitive type"),
         }
     }
+
+    /// Defines an ordering for types.
+    fn type_index(&self) -> usize {
+        match self {
+            Type::Map(_) => 5,
+            Type::Array(a) => match a.is_non_empty() {
+                true => 1,
+                false => 2,
+            },
+            Type::Pair(_) => 6,
+            Type::Object(_) => 4,
+            Type::Ref(_) => 3,
+            Type::Primitive(p) => match p.kind() {
+                PrimitiveTypeKind::Boolean => 8,
+                PrimitiveTypeKind::Integer => 10,
+                PrimitiveTypeKind::Float => 9,
+                PrimitiveTypeKind::String => 7,
+                PrimitiveTypeKind::File => 0,
+            },
+        }
+    }
 }
 
 impl AstNode for Type {
@@ -545,6 +656,31 @@ impl fmt::Display for Type {
     }
 }
 
+impl PartialOrd for Type {
+    fn partial_cmp(&self, other: &Self) -> Option<std::cmp::Ordering> {
+        Some(self.cmp(other))
+    }
+}
+
+impl Ord for Type {
+    fn cmp(&self, other: &Self) -> std::cmp::Ordering {
+        compare_types(self, other)
+    }
+}
+
+/// Compare all variants of Type.
+fn compare_types(a: &Type, b: &Type) -> std::cmp::Ordering {
+    // Check Array, Map, and Pair for sub-types
+    match (a, b) {
+        (Type::Map(a), Type::Map(b)) => a.cmp(b),
+        (Type::Array(a), Type::Array(b)) => a.cmp(b),
+        (Type::Pair(a), Type::Pair(b)) => a.cmp(b),
+        (Type::Ref(a), Type::Ref(b)) => a.cmp(b),
+        (Type::Object(a), Type::Object(b)) => a.cmp(b),
+        _ => a.type_index().cmp(&b.type_index()),
+    }
+}
+
 /// Represents an unbound declaration.
 #[derive(Clone, Debug, PartialEq, Eq)]
 pub struct UnboundDecl(pub(crate) SyntaxNode);
@@ -691,6 +827,20 @@ impl Decl {
             _ => panic!("not an unbound declaration"),
         }
     }
+
+    /// Define an ordering for declarations.
+    fn decl_index(&self) -> usize {
+        match self {
+            Self::Bound(b) => match b.ty().is_optional() {
+                true => 2,
+                false => 3,
+            },
+            Self::Unbound(u) => match u.ty().is_optional() {
+                true => 1,
+                false => 0,
+            },
+        }
+    }
 }
 
 impl AstNode for Decl {
@@ -722,6 +872,33 @@ impl AstNode for Decl {
     }
 }
 
+impl PartialOrd for Decl {
+    fn partial_cmp(&self, other: &Self) -> Option<std::cmp::Ordering> {
+        Some(self.cmp(other))
+    }
+}
+
+impl Ord for Decl {
+    fn cmp(&self, other: &Self) -> std::cmp::Ordering {
+        compare_decl(self, other)
+    }
+}
+
+/// Compare all variants of Decl.
+fn compare_decl(a: &Decl, b: &Decl) -> std::cmp::Ordering {
+    if (matches!(a, Decl::Bound(_))
+        && matches!(b, Decl::Bound(_))
+        && a.ty().is_optional() == b.ty().is_optional())
+        || (matches!(a, Decl::Unbound(_))
+            && matches!(b, Decl::Unbound(_))
+            && a.ty().is_optional() == b.ty().is_optional())
+    {
+        a.ty().cmp(&b.ty())
+    } else {
+        a.decl_index().cmp(&b.decl_index())
+    }
+}
+
 #[cfg(test)]
 mod test {
     use super::*;
diff --git a/wdl-lint/CHANGELOG.md b/wdl-lint/CHANGELOG.md
index 89e00aa7..0e47497c 100644
--- a/wdl-lint/CHANGELOG.md
+++ b/wdl-lint/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * Added the `MissingMetas` and `MissingOutput` lint rules (#96).
 * Added the `PascalCase` lint rule ([#90](https://github.com/stjude-rust-labs/wdl/pull/90)).
 * Added the `ImportPlacement` lint rule ([#89](https://github.com/stjude-rust-labs/wdl/pull/89)).
+* Added the `InputNotSorted` lint rule ([#100](https://github.com/stjude-rust-labs/wdl/pull/100)).
 
 ### Fixed
 
diff --git a/wdl-lint/RULES.md b/wdl-lint/RULES.md
index c82ecf07..1e1eb48f 100644
--- a/wdl-lint/RULES.md
+++ b/wdl-lint/RULES.md
@@ -14,6 +14,7 @@ be out of sync with released packages.
 | `ImportPlacement`                | Clarity                       | Ensures that imports are placed between the version statement and any document items. |
 | `ImportSort`                     | Clarity, Style                | Ensures that imports are sorted lexicographically.                                    |
 | `ImportWhitespace`               | Clarity, Style, Spacing       | Ensures that there is no extraneous whitespace between or within imports.             |
+| `InputNotSorted`                 | Style                         | Ensures that input declarations are sorted                 |
 | `MatchingParameterMeta`          | Completeness                  | Ensures that inputs have a matching entry in a `parameter_meta` section.              |
 | `MissingRuntime`                 | Completeness, Portability     | Ensures that tasks have a runtime section.                                            |
 | `MissingMetas`                   | Completeness, Clarity         | Ensures that tasks have both a meta and a parameter_meta section.                     |
diff --git a/wdl-lint/src/lib.rs b/wdl-lint/src/lib.rs
index 99779953..12a1e8bd 100644
--- a/wdl-lint/src/lib.rs
+++ b/wdl-lint/src/lib.rs
@@ -92,6 +92,7 @@ pub fn rules() -> Vec<Box<dyn Rule>> {
         Box::new(rules::MissingMetasRule),
         Box::new(rules::MissingOutputRule),
         Box::new(rules::ImportSortRule),
+        Box::new(rules::InputNotSortedRule),
         Box::new(rules::LineWidthRule::default()),
     ];
 
diff --git a/wdl-lint/src/rules.rs b/wdl-lint/src/rules.rs
index 3450e795..e8400506 100644
--- a/wdl-lint/src/rules.rs
+++ b/wdl-lint/src/rules.rs
@@ -6,6 +6,7 @@ mod ending_newline;
 mod import_placement;
 mod import_sort;
 mod import_whitespace;
+mod input_not_sorted;
 mod line_width;
 mod matching_parameter_meta;
 mod missing_metas;
@@ -24,6 +25,7 @@ pub use ending_newline::*;
 pub use import_placement::*;
 pub use import_sort::*;
 pub use import_whitespace::*;
+pub use input_not_sorted::*;
 pub use line_width::*;
 pub use matching_parameter_meta::*;
 pub use missing_metas::*;
diff --git a/wdl-lint/src/rules/input_not_sorted.rs b/wdl-lint/src/rules/input_not_sorted.rs
new file mode 100644
index 00000000..3ae51819
--- /dev/null
+++ b/wdl-lint/src/rules/input_not_sorted.rs
@@ -0,0 +1,101 @@
+//! A lint rule for sorting of inputs.
+
+use wdl_ast::span_of;
+use wdl_ast::v1::InputSection;
+use wdl_ast::AstNode;
+use wdl_ast::Diagnostic;
+use wdl_ast::Diagnostics;
+use wdl_ast::Span;
+use wdl_ast::VisitReason;
+use wdl_ast::Visitor;
+
+use crate::Rule;
+use crate::Tag;
+use crate::TagSet;
+
+/// The identifier for the input not sorted rule.
+const ID: &str = "InputSorting";
+
+/// Creates a "input not sorted" diagnostic.
+fn input_not_sorted(span: Span, sorted_inputs: String) -> Diagnostic {
+    Diagnostic::warning("input not sorted")
+        .with_rule(ID)
+        .with_label("input section must be sorted".to_string(), span)
+        .with_fix(format!("sort input statements as: \n{}", sorted_inputs))
+}
+
+/// Detects unsorted input declarations.
+#[derive(Debug, Clone, Copy)]
+pub struct InputNotSortedRule;
+
+impl Rule for InputNotSortedRule {
+    fn id(&self) -> &'static str {
+        ID
+    }
+
+    fn description(&self) -> &'static str {
+        "Ensures that input declarations are sorted."
+    }
+
+    fn explanation(&self) -> &'static str {
+        "Each input declaration section should be sorted. This rule enforces an opinionated \
+         sorting. First sorts by 1. required inputs, 2. optional inputs without defaults, 3. \
+         optional inputs with defaults, and 4. inputs with a default value. Then by the type: 1. \
+         File, 2. Array[*]+, 3. Array[*], 4. struct, 5. Object, 6. Map[*, *], 7. Pair[*, *], 8. \
+         String, 9. Boolean, 10. Float, 11. Int. For ordering of the same compound type (Array[*], \
+         Map[*, *], Pair[*, *]), drop the outermost type (Array, Map, etc.) and recursively apply \
+         above sorting on the first inner type *, with ties broken by the second inner type. \
+         Continue this pattern as far as possible. Once this ordering is satisfied, it is up to \
+         the developer for final order of inputs of the same type."
+    }
+
+    fn tags(&self) -> TagSet {
+        TagSet::new(&[Tag::Style, Tag::Clarity, Tag::Sorting])
+    }
+
+    fn visitor(&self) -> Box<dyn Visitor<State = Diagnostics>> {
+        Box::new(InputNotSortedVisitor)
+    }
+}
+
+/// Implements the visitor for the input not sorted rule.
+struct InputNotSortedVisitor;
+
+impl Visitor for InputNotSortedVisitor {
+    type State = Diagnostics;
+
+    fn input_section(
+        &mut self,
+        state: &mut Self::State,
+        reason: VisitReason,
+        input: &InputSection,
+    ) {
+        if reason == VisitReason::Exit {
+            return;
+        }
+
+        // Get input section declarations
+        let decls: Vec<_> = input.declarations().collect();
+        let mut sorted_decls = decls.clone();
+        sorted_decls.sort();
+
+        let input_string: String = sorted_decls
+            .clone()
+            .into_iter()
+            .map(|decl| decl.syntax().text().to_string() + "\n")
+            .collect::<String>();
+        let mut errors = 0;
+
+        decls
+            .into_iter()
+            .zip(sorted_decls)
+            .for_each(|(decl, sorted_decl)| {
+                if decl != sorted_decl {
+                    errors += 1;
+                }
+            });
+        if errors > 0 {
+            state.add(input_not_sorted(span_of(input), input_string));
+        }
+    }
+}
diff --git a/wdl-lint/src/tags.rs b/wdl-lint/src/tags.rs
index a33703f1..8ea4752f 100644
--- a/wdl-lint/src/tags.rs
+++ b/wdl-lint/src/tags.rs
@@ -24,6 +24,9 @@ pub enum Tag {
 
     /// Rules associated with the correctness of a document.
     Correctness,
+
+    /// Rules associated with sorting of document elements.
+    Sorting,
 }
 
 impl std::fmt::Display for Tag {
@@ -36,6 +39,7 @@ impl std::fmt::Display for Tag {
             Self::Clarity => write!(f, "Clarity"),
             Self::Portability => write!(f, "Portability"),
             Self::Correctness => write!(f, "Correctness"),
+            Self::Sorting => write!(f, "Sorting"),
         }
     }
 }
diff --git a/wdl-lint/src/v1.rs b/wdl-lint/src/v1.rs
index 9c70e405..f1594f65 100644
--- a/wdl-lint/src/v1.rs
+++ b/wdl-lint/src/v1.rs
@@ -10,6 +10,7 @@ mod double_quotes;
 mod ending_newline;
 mod import_placement;
 mod import_whitespace;
+mod input_not_sorted;
 mod matching_parameter_meta;
 mod missing_metas;
 mod missing_output;
@@ -26,6 +27,7 @@ pub use double_quotes::*;
 pub use ending_newline::*;
 pub use import_placement::*;
 pub use import_whitespace::*;
+pub use input_not_sorted::*;
 pub use matching_parameter_meta::*;
 pub use missing_metas::*;
 pub use missing_output::*;
@@ -83,6 +85,7 @@ pub fn rules() -> Vec<Box<dyn Rule>> {
         Box::new(PascalCaseRule),
         Box::new(MissingMetasRule),
         Box::new(MissingOutputRule),
+        Box::new(InputNotSortedRule),
     ];
 
     // Ensure all the rule ids are unique and pascal case
diff --git a/wdl-lint/tests/lints/input-not-sorted/source.errors b/wdl-lint/tests/lints/input-not-sorted/source.errors
new file mode 100644
index 00000000..17efafaf
--- /dev/null
+++ b/wdl-lint/tests/lints/input-not-sorted/source.errors
@@ -0,0 +1,70 @@
+warning[InputSorting]: input not sorted
+   ┌─ tests/lints/input-not-sorted/source.wdl:34:5
+   │  
+34 │ ╭     input {
+35 │ │         String g = "hello"
+36 │ │         Int? f = 2
+37 │ │         Int? e
+   · │
+56 │ │         mystruct u
+57 │ │     }
+   │ ╰─────^ input section must be sorted
+   │  
+   = fix: sort input statements as: 
+     File t
+     File b
+     Array[String]+ p
+     Array[String] q
+     mystruct u
+     Object v
+     Map[String, File] s
+     Pair[File, Int] j
+     Pair[String, File] n
+     Pair[String, Int] o
+     Pair[Int, File] i
+     String a
+     Int c
+     Array[String]? h
+     Array[Int]? d
+     Map[String, File]? r
+     Map[String, Array[Int]]? l
+     Map[String, Int]? k
+     Map[Int, String]? m
+     Int? e
+     Int? f = 2
+     String g = "hello"
+
+warning[InputSorting]: input not sorted
+    ┌─ tests/lints/input-not-sorted/source.wdl:85:5
+    │  
+ 85 │ ╭     input {
+ 86 │ │         String g = "hello"
+ 87 │ │         Int? f = 2
+ 88 │ │         Int? e
+    · │
+105 │ │         Array[String]+ p
+106 │ │     }
+    │ ╰─────^ input section must be sorted
+    │  
+    = fix: sort input statements as: 
+      File t
+      File b
+      Array[String]+ p
+      Array[String] q
+      Map[String, File] s
+      Pair[File, Int] j
+      Pair[String, File] n
+      Pair[String, Int] o
+      Pair[Int, File] i
+      String a
+      Int c
+      Array[String]? h
+      Array[Int]? d
+      Map[String, File]? r
+      Map[String, Array[Int]]? l
+      Map[String, Int]? k
+      Map[Int, String]? m
+      Int? e
+      Int? f = 2
+      String g = "hello"
+
diff --git a/wdl-lint/tests/lints/input-not-sorted/source.wdl b/wdl-lint/tests/lints/input-not-sorted/source.wdl
new file mode 100644
index 00000000..43c24841
--- /dev/null
+++ b/wdl-lint/tests/lints/input-not-sorted/source.wdl
@@ -0,0 +1,111 @@
+version 1.1
+
+struct Mystruct {
+    String a
+    Int b
+}
+
+workflow foo {
+    meta {}
+    parameter_meta {
+        a: ""
+        b: ""
+        c: ""
+        d: ""
+        e: ""
+        f: ""
+        g: ""
+        h: ""
+        i: ""
+        j: ""
+        k: ""
+        l: ""
+        m: ""
+        n: ""
+        o: ""
+        p: ""
+        q: ""
+        r: ""
+        s: ""
+        t: ""
+        u: ""
+        v: ""
+    }
+    input {
+        String g = "hello"
+        Int? f = 2
+        Int? e
+        Int c
+        Array[String]? h
+        File t
+        String a
+        Pair[Int, File] i
+        File b
+        Pair[String, Int] o
+        Pair[File, Int] j
+        Array[Int]? d
+        Array[String] q
+        Object v
+        Map[String, Int]? k
+        Map[String, Array[Int]]? l
+        Map[Int, String]? m
+        Map[String, File]? r
+        Map[String, File] s
+        Pair[String, File] n
+        Array[String]+ p
+        mystruct u
+    }
+    output {}
+}
+
+task bar {
+    meta {}
+    parameter_meta {
+        a: ""
+        b: ""
+        c: ""
+        d: ""
+        e: ""
+        f: ""
+        g: ""
+        h: ""
+        i: ""
+        j: ""
+        k: ""
+        l: ""
+        m: ""
+        n: ""
+        o: ""
+        p: ""
+        q: ""
+        r: ""
+        s: ""
+        t: ""
+    }
+    input {
+        String g = "hello"
+        Int? f = 2
+        Int? e
+        Int c
+        Array[String]? h
+        File t
+        String a
+        Pair[Int, File] i
+        File b
+        Pair[String, Int] o
+        Pair[File, Int] j
+        Array[Int]? d
+        Array[String] q
+        Map[String, Int]? k
+        Map[String, Array[Int]]? l
+        Map[Int, String]? m
+        Map[String, File]? r
+        Map[String, File] s
+        Pair[String, File] n
+        Array[String]+ p
+    }
+    command <<<
+    >>>
+    runtime {}
+    output {}
+}