From 26a6448ed77ec31a0c3e804142157e416ecef25e Mon Sep 17 00:00:00 2001
From: Clay McLeod <clay.l.mcleod@gmail.com>
Date: Tue, 16 Jul 2024 13:55:43 -0500
Subject: [PATCH] fix: fixes the `line_width` rule

---
 Arena.toml                                    | 869 +-----------------
 Gauntlet.toml                                 |  16 +-
 wdl-lint/src/rules/line_width.rs              |  55 +-
 wdl-lint/src/visitor.rs                       |   1 +
 wdl-lint/tests/lints/line-width/source.errors |  16 +
 wdl-lint/tests/lints/line-width/source.wdl    |  53 ++
 6 files changed, 105 insertions(+), 905 deletions(-)
 create mode 100644 wdl-lint/tests/lints/line-width/source.errors
 create mode 100644 wdl-lint/tests/lints/line-width/source.wdl

diff --git a/Arena.toml b/Arena.toml
index b88bb4ef1..b1ec7f37a 100644
--- a/Arena.toml
+++ b/Arena.toml
@@ -12,7 +12,7 @@ commit_hash = "c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2"
 
 [repositories."stjudecloud/workflows"]
 identifier = "stjudecloud/workflows"
-commit_hash = "833b97fb582fe7d4f6df9d29a645d0289f1fc92e"
+commit_hash = "ec7cb3e21ef900d71db040943d7e14e94fa3b567"
 filters = ["/template/task-templates.wdl"]
 
 [[diagnostics]]
@@ -35,21 +35,11 @@ document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
 message = "ww-fastq-to-cram.wdl:134:6: warning[SnakeCase]: task name `ValidateCram` is not snake_case"
 permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L134"
 
-[[diagnostics]]
-document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
-message = "ww-fastq-to-cram.wdl:14:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L14"
-
 [[diagnostics]]
 document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
 message = "ww-fastq-to-cram.wdl:165:5: note[MatchingParameterMeta]: task `ValidateCram` has an extraneous parameter metadata key named `validation`"
 permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L165"
 
-[[diagnostics]]
-document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
-message = "ww-fastq-to-cram.wdl:16:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L16"
-
 [[diagnostics]]
 document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
 message = "ww-fastq-to-cram.wdl:170:6: note[MissingMetas]: task `MergeBamsToCram` is missing a `meta` section"
@@ -100,31 +90,16 @@ document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
 message = "ww-fastq-to-cram.wdl:2:1: note[PreambleWhitespace]: expected a blank line after the version statement"
 permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L2"
 
-[[diagnostics]]
-document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
-message = "ww-fastq-to-cram.wdl:34:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L34"
-
 [[diagnostics]]
 document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
 message = "ww-fastq-to-cram.wdl:35:112: note[CallInputSpacing]: call input not properly spaced"
 permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L35"
 
-[[diagnostics]]
-document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
-message = "ww-fastq-to-cram.wdl:35:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L35"
-
 [[diagnostics]]
 document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
 message = "ww-fastq-to-cram.wdl:48:116: note[CallInputSpacing]: call input not properly spaced"
 permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L48"
 
-[[diagnostics]]
-document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
-message = "ww-fastq-to-cram.wdl:48:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L48"
-
 [[diagnostics]]
 document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
 message = "ww-fastq-to-cram.wdl:56:67: note[CallInputSpacing]: call input not properly spaced"
@@ -240,11 +215,6 @@ document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
 message = "ww-star-deseq2.wdl:159:6: warning[SnakeCase]: task name `STARalignTwoPass` is not snake_case"
 permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L159"
 
-[[diagnostics]]
-document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
-message = "ww-star-deseq2.wdl:183:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L183"
-
 [[diagnostics]]
 document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
 message = "ww-star-deseq2.wdl:192:10: warning[SnakeCase]: output name `geneCounts` is not snake_case"
@@ -290,11 +260,6 @@ document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
 message = "ww-star-deseq2.wdl:218:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `SJout`"
 permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L218"
 
-[[diagnostics]]
-document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
-message = "ww-star-deseq2.wdl:224:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L224"
-
 [[diagnostics]]
 document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
 message = "ww-star-deseq2.wdl:225:6: note[MissingMetas]: task `RNASeQC` is missing a `meta` section"
@@ -740,11 +705,6 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:306:17: warning[SnakeCase]: input name `known_indels_sites_VCFs` is not snake_case"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L306"
 
-[[diagnostics]]
-document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
-message = "ww-vc-trio.wdl:336:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L336"
-
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:342:10: warning[SnakeCase]: output name `sortOrder` is not snake_case"
@@ -800,11 +760,6 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:409:10: warning[SnakeCase]: output name `meanQC` is not snake_case"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L409"
 
-[[diagnostics]]
-document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
-message = "ww-vc-trio.wdl:40:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L40"
-
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:420:6: note[MissingMetas]: task `BwaMem` is missing both meta and parameter_meta sections"
@@ -820,11 +775,6 @@ 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/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/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"
-permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L441"
-
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:456:6: note[MissingMetas]: task `CollectHsMetrics` is missing both meta and parameter_meta sections"
@@ -900,16 +850,6 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:49:53: warning[Whitespace]: line contains trailing whitespace"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L49"
 
-[[diagnostics]]
-document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
-message = "ww-vc-trio.wdl:4:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L4"
-
-[[diagnostics]]
-document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
-message = "ww-vc-trio.wdl:503:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L503"
-
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:507:10: warning[SnakeCase]: output name `consensusTSV` is not snake_case"
@@ -1025,11 +965,6 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:64:12: warning[SnakeCase]: private declaration name `sampleName` is not snake_case"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L64"
 
-[[diagnostics]]
-document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
-message = "ww-vc-trio.wdl:650:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L650"
-
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:65:12: warning[SnakeCase]: private declaration name `molecularID` is not snake_case"
@@ -1060,21 +995,6 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:709:6: warning[SnakeCase]: task name `MarkDuplicates` is not snake_case"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L709"
 
-[[diagnostics]]
-document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
-message = "ww-vc-trio.wdl:717:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L717"
-
-[[diagnostics]]
-document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
-message = "ww-vc-trio.wdl:718:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L718"
-
-[[diagnostics]]
-document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
-message = "ww-vc-trio.wdl:719:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L719"
-
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:72:22: note[CallInputSpacing]: call input not properly spaced"
@@ -1095,11 +1015,6 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:771:2: warning[EndingNewline]: multiple empty lines at the end of file"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L771"
 
-[[diagnostics]]
-document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
-message = "ww-vc-trio.wdl:7:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L7"
-
 [[diagnostics]]
 document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:80:18: note[CallInputSpacing]: call input not properly spaced"
@@ -1115,787 +1030,7 @@ document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
 message = "ww-vc-trio.wdl:98:29: note[CallInputSpacing]: call input not properly spaced"
 permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L98"
 
-[[diagnostics]]
-document = "stjudecloud/workflows:/data_structures/flag_filter.wdl"
-message = "flag_filter.wdl:116:5: warning[RuntimeSectionKeys]: the following runtime key is not reserved in the WDL v1.1 specification: `disk`; therefore, its inclusion in the `runtime` section is deprecated"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/flag_filter.wdl/#L116"
-
-[[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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L12"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/data_structures/read_group.wdl"
-message = "read_group.wdl:130:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L130"
-
-[[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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L13"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/data_structures/read_group.wdl"
-message = "read_group.wdl:140:5: warning[RuntimeSectionKeys]: the following runtime key is not reserved in the WDL v1.1 specification: `disk`; therefore, its inclusion in the `runtime` section is deprecated"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L140"
-
-[[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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L14"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/data_structures/read_group.wdl"
-message = "read_group.wdl:174:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L174"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/data_structures/read_group.wdl"
-message = "read_group.wdl:183:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L183"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/data_structures/read_group.wdl"
-message = "read_group.wdl:207:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L207"
-
-[[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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L2"
-
-[[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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L3"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/data_structures/read_group.wdl"
-message = "read_group.wdl:420:5: warning[RuntimeSectionKeys]: the following runtime key is not reserved in the WDL v1.1 specification: `disk`; therefore, its inclusion in the `runtime` section is deprecated"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L420"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/data_structures/read_group.wdl"
-message = "read_group.wdl:7:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L7"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/data_structures/read_group.wdl"
-message = "read_group.wdl:89:5: warning[RuntimeSectionKeys]: the following runtime key is not reserved in the WDL v1.1 specification: `disk`; therefore, its inclusion in the `runtime` section is deprecated"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L89"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/data_structures/read_group.wdl"
-message = "read_group.wdl:8:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/data_structures/read_group.wdl/#L8"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/tools/arriba.wdl"
-message = "arriba.wdl:140:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/tools/arriba.wdl/#L140"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/tools/arriba.wdl"
-message = "arriba.wdl:143:1: note[LineWidth]: line exceeds maximum width of 90"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/tools/arriba.wdl/#L143"
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-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L47"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard.wdl"
-message = "rnaseq-standard.wdl:179:5: warning[RuntimeSectionKeys]: the following runtime key is not reserved in the WDL v1.1 specification: `disk`; therefore, its inclusion in the `runtime` section is deprecated"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/workflows/rnaseq/rnaseq-standard.wdl/#L179"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard.wdl"
-message = "rnaseq-standard.wdl:94:10: note[Todo]: remaining `TODO` item found"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/workflows/rnaseq/rnaseq-standard.wdl/#L94"
-
-[[diagnostics]]
-document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
-message = "10x-bam-to-fastqs.wdl:130:5: warning[RuntimeSectionKeys]: the following runtime key is not reserved in the WDL v1.1 specification: `disk`; therefore, its inclusion in the `runtime` section is deprecated"
-permalink = "https://github.com/stjudecloud/workflows/blob/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L130"
-
-[[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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L38"
-
-[[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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/workflows/scrnaseq/scrnaseq-standard.wdl/#L28"
-
-[[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/833b97fb582fe7d4f6df9d29a645d0289f1fc92e/workflows/scrnaseq/scrnaseq-standard.wdl/#L5"
+permalink = "https://github.com/stjudecloud/workflows/blob/ec7cb3e21ef900d71db040943d7e14e94fa3b567/tools/estimate.wdl/#L39"
diff --git a/Gauntlet.toml b/Gauntlet.toml
index b81ed0012..43780bc06 100644
--- a/Gauntlet.toml
+++ b/Gauntlet.toml
@@ -24,7 +24,7 @@ commit_hash = "4e7fdfa7992dd1bf4c4721e77c81e4d7b8ecf4fe"
 
 [repositories."broadinstitute/warp"]
 identifier = "broadinstitute/warp"
-commit_hash = "9942eed7d6c8aba87ddf096fc77cddc6f5052e54"
+commit_hash = "25a98392991857f4a8be429075c0c7496834aa88"
 
 [repositories."chanzuckerberg/czid-workflows"]
 identifier = "chanzuckerberg/czid-workflows"
@@ -44,7 +44,7 @@ commit_hash = "c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2"
 
 [repositories."stjudecloud/workflows"]
 identifier = "stjudecloud/workflows"
-commit_hash = "833b97fb582fe7d4f6df9d29a645d0289f1fc92e"
+commit_hash = "ec7cb3e21ef900d71db040943d7e14e94fa3b567"
 filters = ["/template/task-templates.wdl"]
 
 [repositories."theiagen/public_health_bioinformatics"]
@@ -384,32 +384,32 @@ permalink = "https://github.com/broadinstitute/palantir-workflows/blob/4e7fdfa79
 [[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/9942eed7d6c8aba87ddf096fc77cddc6f5052e54/pipelines/skylab/scATAC/scATAC.wdl/#L203"
+permalink = "https://github.com/broadinstitute/warp/blob/25a98392991857f4a8be429075c0c7496834aa88/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/9942eed7d6c8aba87ddf096fc77cddc6f5052e54/tasks/broad/GermlineVariantDiscovery.wdl/#L140"
+permalink = "https://github.com/broadinstitute/warp/blob/25a98392991857f4a8be429075c0c7496834aa88/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/9942eed7d6c8aba87ddf096fc77cddc6f5052e54/tasks/broad/GermlineVariantDiscovery.wdl/#L67"
+permalink = "https://github.com/broadinstitute/warp/blob/25a98392991857f4a8be429075c0c7496834aa88/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/9942eed7d6c8aba87ddf096fc77cddc6f5052e54/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L814"
+permalink = "https://github.com/broadinstitute/warp/blob/25a98392991857f4a8be429075c0c7496834aa88/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/9942eed7d6c8aba87ddf096fc77cddc6f5052e54/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L866"
+permalink = "https://github.com/broadinstitute/warp/blob/25a98392991857f4a8be429075c0c7496834aa88/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/9942eed7d6c8aba87ddf096fc77cddc6f5052e54/tests/cemba/pr/CheckCembaOutputs.wdl/#L1"
+permalink = "https://github.com/broadinstitute/warp/blob/25a98392991857f4a8be429075c0c7496834aa88/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..176f6db7b 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 +48,23 @@ 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();
+
+            // let width = UnicodeWidthStr::width(&)
+
+            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 +73,8 @@ 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 +85,7 @@ 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 +134,7 @@ 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 +143,6 @@ 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/src/visitor.rs b/wdl-lint/src/visitor.rs
index 06f6e9316..6e92436a5 100644
--- a/wdl-lint/src/visitor.rs
+++ b/wdl-lint/src/visitor.rs
@@ -85,6 +85,7 @@ impl LintVisitor {
         if reason == VisitReason::Enter {
             let exceptions = self.exceptions_for(state, node);
             if !exceptions.is_empty() {
+                println!("Pushing {exceptions:?} for {node}");
                 self.exceptions.push((start, exceptions));
             }
         }
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..2cdf6dd4a
--- /dev/null
+++ b/wdl-lint/tests/lints/line-width/source.errors
@@ -0,0 +1,16 @@
+note[LineWidth]: line exceeds maximum width of 90
+   ┌─ tests/lints/line-width/source.wdl:12:2
+   │
+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:14:2
+   │
+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
+
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..6f775710d
--- /dev/null
+++ b/wdl-lint/tests/lints/line-width/source.wdl
@@ -0,0 +1,53 @@
+#@ 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 {}
+
+    #@ 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.