diff --git a/Arena.toml b/Arena.toml
index c6c8421d2..68c9a25ff 100644
--- a/Arena.toml
+++ b/Arena.toml
@@ -12,7 +12,7 @@ commit_hash = "c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2"
 
 [repositories."stjudecloud/workflows"]
 identifier = "stjudecloud/workflows"
-commit_hash = "ec7cb3e21ef900d71db040943d7e14e94fa3b567"
+commit_hash = "129060215443bbd1b67c4d3d149d48acdab90ef2"
 filters = ["/template/task-templates.wdl"]
 
 [[diagnostics]]
@@ -1118,79 +1118,79 @@ permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f87
 [[diagnostics]]
 document = "stjudecloud/workflows:/data_structures/read_group.wdl"
 message = "read_group.wdl:134:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/data_structures/read_group.wdl/#L134"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/data_structures/read_group.wdl/#L134"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/arriba.wdl"
 message = "arriba.wdl:147:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/tools/arriba.wdl/#L147"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L147"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/estimate.wdl"
 message = "estimate.wdl:39:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/tools/estimate.wdl/#L39"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/estimate.wdl/#L39"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/gatk4.wdl"
 message = "gatk4.wdl:127:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/tools/gatk4.wdl/#L127"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L127"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/gatk4.wdl"
 message = "gatk4.wdl:194:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/tools/gatk4.wdl/#L194"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L194"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/gatk4.wdl"
 message = "gatk4.wdl:280:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/tools/gatk4.wdl/#L280"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L280"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/htseq.wdl"
 message = "htseq.wdl:163:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/tools/htseq.wdl/#L163"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L163"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/ngsderive.wdl"
 message = "ngsderive.wdl:239:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/tools/ngsderive.wdl/#L239"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L239"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/star.wdl"
 message = "star.wdl:632:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/tools/star.wdl/#L632"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L632"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/util.wdl"
 message = "util.wdl:458:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/tools/util.wdl/#L458"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L458"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/tools/util.wdl"
 message = "util.wdl:713:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/tools/util.wdl/#L713"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L713"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/chipseq/chipseq-standard.wdl"
 message = "chipseq-standard.wdl:10:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/workflows/chipseq/chipseq-standard.wdl/#L10"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/chipseq/chipseq-standard.wdl/#L10"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/chipseq/chipseq-standard.wdl"
 message = "chipseq-standard.wdl:11:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/workflows/chipseq/chipseq-standard.wdl/#L11"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/chipseq/chipseq-standard.wdl/#L11"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/chipseq/chipseq-standard.wdl"
 message = "chipseq-standard.wdl:12:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/workflows/chipseq/chipseq-standard.wdl/#L12"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/chipseq/chipseq-standard.wdl/#L12"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/general/alignment-post.wdl"
 message = "alignment-post.wdl:6:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/workflows/general/alignment-post.wdl/#L6"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/general/alignment-post.wdl/#L6"
 
 [[diagnostics]]
 document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
 message = "quality-check-standard.wdl:111:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/workflows/qc/quality-check-standard.wdl/#L111"
+permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L111"
diff --git a/Gauntlet.toml b/Gauntlet.toml
index 43780bc06..3d92b8a03 100644
--- a/Gauntlet.toml
+++ b/Gauntlet.toml
@@ -20,11 +20,11 @@ commit_hash = "4536dd2c6719b86f4c50348f0ce354818260cadb"
 
 [repositories."broadinstitute/palantir-workflows"]
 identifier = "broadinstitute/palantir-workflows"
-commit_hash = "4e7fdfa7992dd1bf4c4721e77c81e4d7b8ecf4fe"
+commit_hash = "efb0eadd70fe21fe9484a310f12a6c54b752db43"
 
 [repositories."broadinstitute/warp"]
 identifier = "broadinstitute/warp"
-commit_hash = "25a98392991857f4a8be429075c0c7496834aa88"
+commit_hash = "16d9ae6fc19071acd3541ac2950908d2cc2d03bd"
 
 [repositories."chanzuckerberg/czid-workflows"]
 identifier = "chanzuckerberg/czid-workflows"
@@ -44,12 +44,12 @@ commit_hash = "c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2"
 
 [repositories."stjudecloud/workflows"]
 identifier = "stjudecloud/workflows"
-commit_hash = "ec7cb3e21ef900d71db040943d7e14e94fa3b567"
+commit_hash = "129060215443bbd1b67c4d3d149d48acdab90ef2"
 filters = ["/template/task-templates.wdl"]
 
 [repositories."theiagen/public_health_bioinformatics"]
 identifier = "theiagen/public_health_bioinformatics"
-commit_hash = "42a06efca2be1935cc8b5936b1fa9164e5646b80"
+commit_hash = "6d406b65a1cfa0b7e1042da2e750cbbf91531c92"
 
 [[diagnostics]]
 document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl"
@@ -379,37 +379,37 @@ permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026
 [[diagnostics]]
 document = "broadinstitute/palantir-workflows:/HaplotypeMap/BuildHaplotypeMap.wdl"
 message = "BuildHaplotypeMap.wdl:17:1: error: a WDL document must start with a version statement"
-permalink = "https://github.com/broadinstitute/palantir-workflows/blob/4e7fdfa7992dd1bf4c4721e77c81e4d7b8ecf4fe/HaplotypeMap/BuildHaplotypeMap.wdl/#L17"
+permalink = "https://github.com/broadinstitute/palantir-workflows/blob/efb0eadd70fe21fe9484a310f12a6c54b752db43/HaplotypeMap/BuildHaplotypeMap.wdl/#L17"
 
 [[diagnostics]]
 document = "broadinstitute/warp:/pipelines/skylab/scATAC/scATAC.wdl"
 message = "scATAC.wdl:203:9: error: duplicate key `cpu` in runtime section"
-permalink = "https://github.com/broadinstitute/warp/blob/25a98392991857f4a8be429075c0c7496834aa88/pipelines/skylab/scATAC/scATAC.wdl/#L203"
+permalink = "https://github.com/broadinstitute/warp/blob/16d9ae6fc19071acd3541ac2950908d2cc2d03bd/pipelines/skylab/scATAC/scATAC.wdl/#L203"
 
 [[diagnostics]]
 document = "broadinstitute/warp:/tasks/broad/GermlineVariantDiscovery.wdl"
 message = "GermlineVariantDiscovery.wdl:140:32: error: expected string, but found integer"
-permalink = "https://github.com/broadinstitute/warp/blob/25a98392991857f4a8be429075c0c7496834aa88/tasks/broad/GermlineVariantDiscovery.wdl/#L140"
+permalink = "https://github.com/broadinstitute/warp/blob/16d9ae6fc19071acd3541ac2950908d2cc2d03bd/tasks/broad/GermlineVariantDiscovery.wdl/#L140"
 
 [[diagnostics]]
 document = "broadinstitute/warp:/tasks/broad/GermlineVariantDiscovery.wdl"
 message = "GermlineVariantDiscovery.wdl:67:32: error: expected string, but found integer"
-permalink = "https://github.com/broadinstitute/warp/blob/25a98392991857f4a8be429075c0c7496834aa88/tasks/broad/GermlineVariantDiscovery.wdl/#L67"
+permalink = "https://github.com/broadinstitute/warp/blob/16d9ae6fc19071acd3541ac2950908d2cc2d03bd/tasks/broad/GermlineVariantDiscovery.wdl/#L67"
 
 [[diagnostics]]
 document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl"
 message = "UltimaGenomicsWholeGenomeGermlineTasks.wdl:814:27: error: expected string, but found integer"
-permalink = "https://github.com/broadinstitute/warp/blob/25a98392991857f4a8be429075c0c7496834aa88/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L814"
+permalink = "https://github.com/broadinstitute/warp/blob/16d9ae6fc19071acd3541ac2950908d2cc2d03bd/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L814"
 
 [[diagnostics]]
 document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl"
 message = "UltimaGenomicsWholeGenomeGermlineTasks.wdl:866:27: error: expected string, but found integer"
-permalink = "https://github.com/broadinstitute/warp/blob/25a98392991857f4a8be429075c0c7496834aa88/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L866"
+permalink = "https://github.com/broadinstitute/warp/blob/16d9ae6fc19071acd3541ac2950908d2cc2d03bd/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L866"
 
 [[diagnostics]]
 document = "broadinstitute/warp:/tests/cemba/pr/CheckCembaOutputs.wdl"
 message = "CheckCembaOutputs.wdl:1:1: error: a WDL document must start with a version statement"
-permalink = "https://github.com/broadinstitute/warp/blob/25a98392991857f4a8be429075c0c7496834aa88/tests/cemba/pr/CheckCembaOutputs.wdl/#L1"
+permalink = "https://github.com/broadinstitute/warp/blob/16d9ae6fc19071acd3541ac2950908d2cc2d03bd/tests/cemba/pr/CheckCembaOutputs.wdl/#L1"
 
 [[diagnostics]]
 document = "chanzuckerberg/czid-workflows:/workflows/index-generation/index-generation.wdl"
diff --git a/wdl-lint/src/rules/line_width.rs b/wdl-lint/src/rules/line_width.rs
index fb5f66bbe..7e7a0c7e3 100644
--- a/wdl-lint/src/rules/line_width.rs
+++ b/wdl-lint/src/rules/line_width.rs
@@ -27,14 +27,14 @@ fn line_too_long(span: Span, max_width: usize) -> Diagnostic {
 }
 
 /// Detects lines that exceed a certain width.
-#[derive(Debug, Clone, Copy)]
+#[derive(Clone, Copy, Debug)]
 pub struct LineWidthRule {
     /// The maximum width of a line.
     max_width: usize,
-    /// The offset of the previous newline.
-    prev_newline_offset: usize,
+    /// The offset of the last newline character seen (if it exists).
+    previous_newline_offset: Option<usize>,
     /// Whether we are in a section that should be ignored.
-    should_ignore: bool,
+    ignored_section: bool,
 }
 
 impl LineWidthRule {
@@ -48,27 +48,21 @@ impl LineWidthRule {
 
     /// Detects lines that exceed a certain width.
     fn detect_line_too_long(&mut self, state: &mut Diagnostics, text: &str, start: usize) {
-        let mut cur_newline_offset = start;
-        text.char_indices().for_each(|(i, c)| {
-            if c == '\n' {
-                cur_newline_offset = start + i;
-                if self.should_ignore {
-                    self.prev_newline_offset = cur_newline_offset + 1;
-                    return;
-                }
-
-                if cur_newline_offset - self.prev_newline_offset > self.max_width {
-                    state.add(line_too_long(
-                        Span::new(
-                            self.prev_newline_offset,
-                            cur_newline_offset - self.prev_newline_offset,
-                        ),
-                        self.max_width,
-                    ));
-                }
-                self.prev_newline_offset = cur_newline_offset + 1;
+        for offset in text
+            .char_indices()
+            .filter(|(_, c)| *c == '\n')
+            .map(|(offset, _)| offset)
+        {
+            let current_offset = start + offset;
+            let previous_offset = self.previous_newline_offset.unwrap_or_default();
+
+            if !self.ignored_section && current_offset - previous_offset > self.max_width {
+                let span = Span::new(previous_offset, current_offset - previous_offset);
+                state.add(line_too_long(span, self.max_width));
             }
-        });
+
+            self.previous_newline_offset = Some(current_offset + 1);
+        }
     }
 }
 
@@ -77,8 +71,8 @@ impl Default for LineWidthRule {
     fn default() -> Self {
         Self {
             max_width: 90,
-            prev_newline_offset: 0,
-            should_ignore: false,
+            previous_newline_offset: None,
+            ignored_section: false,
         }
     }
 }
@@ -89,8 +83,7 @@ impl Rule for LineWidthRule {
     }
 
     fn description(&self) -> &'static str {
-        "Ensures that lines do not exceed a certain width. That width is currently set to 90 \
-         characters."
+        "Ensures that lines do not exceed a certain width."
     }
 
     fn explanation(&self) -> &'static str {
@@ -139,7 +132,7 @@ impl Visitor for LineWidthRule {
         reason: VisitReason,
         _: &v1::MetadataSection,
     ) {
-        self.should_ignore = matches!(reason, VisitReason::Enter);
+        self.ignored_section = matches!(reason, VisitReason::Enter);
     }
 
     fn parameter_metadata_section(
@@ -148,6 +141,6 @@ impl Visitor for LineWidthRule {
         reason: VisitReason,
         _: &v1::ParameterMetadataSection,
     ) {
-        self.should_ignore = matches!(reason, VisitReason::Enter);
+        self.ignored_section = matches!(reason, VisitReason::Enter);
     }
 }
diff --git a/wdl-lint/tests/lints/line-width/source.errors b/wdl-lint/tests/lints/line-width/source.errors
new file mode 100644
index 000000000..9979a9366
--- /dev/null
+++ b/wdl-lint/tests/lints/line-width/source.errors
@@ -0,0 +1,46 @@
+note[LineWidth]: line exceeds maximum width of 90
+   ┌─ tests/lints/line-width/source.wdl:12:1
+   │
+12 │             this is going to be a really long line that is almost certainly going to be longer than the maximum line length I would hope /
+   │ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+   │
+   = fix: split the line into multiple lines
+
+note[LineWidth]: line exceeds maximum width of 90
+   ┌─ tests/lints/line-width/source.wdl:14:1
+   │
+14 │             this line is also going to be very very very long just to trip up our maximum line lint /
+   │ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+   │
+   = fix: split the line into multiple lines
+
+note[LineWidth]: line exceeds maximum width of 90
+   ┌─ tests/lints/line-width/source.wdl:31:1
+   │  
+31 │ ╭     command <<<
+32 │ │         bin /
+33 │ │             this is going to be a really long line that is not going to trip up our maximum line lint because it is excepted /
+34 │ │             some other /
+   · │
+37 │ │             options
+38 │ │     >>>
+   │ ╰───────^
+   │  
+   = fix: split the line into multiple lines
+
+note[LineWidth]: line exceeds maximum width of 90
+   ┌─ tests/lints/line-width/source.wdl:49:1
+   │
+49 │     command <<< this is a task that has a very very very long command section on the first line. >>>
+   │ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+   │
+   = fix: split the line into multiple lines
+
+note[LineWidth]: line exceeds maximum width of 90
+   ┌─ tests/lints/line-width/source.wdl:55:1
+   │
+55 │ # Here is a very very very very very very very very very long comment that should absolutely eclipse 90 characters.
+   │ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+   │
+   = fix: split the line into multiple lines
+
diff --git a/wdl-lint/tests/lints/line-width/source.wdl b/wdl-lint/tests/lints/line-width/source.wdl
new file mode 100644
index 000000000..bb46033c0
--- /dev/null
+++ b/wdl-lint/tests/lints/line-width/source.wdl
@@ -0,0 +1,55 @@
+#@ except: DescriptionMissing, RuntimeSectionKeys
+
+version 1.1
+
+task task_a {
+    meta {}
+    parameter_meta {}
+    input {}
+
+    command <<<
+        bin \
+            this is going to be a really long line that is almost certainly going to be longer than the maximum line length I would hope \
+            some other \
+            this line is also going to be very very very long just to trip up our maximum line lint \
+            shorter \
+            options
+    >>>
+
+    output {}
+    runtime {}
+}
+
+task task_b {
+    meta {}
+    parameter_meta {}
+    input {}
+
+    # This except currently causes the entire command block to fail.
+    # That will be fixed in the future when we fix how excepting works.
+    #@ except: LineWidth
+    command <<<
+        bin \
+            this is going to be a really long line that is not going to trip up our maximum line lint because it is excepted \
+            some other \
+            this line is also going to be very very very long but it will also not trip up our maximum line line because it is excepted \
+            shorter \
+            options
+    >>>
+
+    output {}
+    runtime {}
+}
+
+task task_c {
+    meta {}
+    parameter_meta {}
+    input {}
+
+    command <<< this is a task that has a very very very long command section on the first line. >>>
+
+    output {}
+    runtime {}
+}
+
+# Here is a very very very very very very very very very long comment that should absolutely eclipse 90 characters.