diff --git a/Gauntlet.toml b/Gauntlet.toml
index 240b17c4..54c0f182 100644
--- a/Gauntlet.toml
+++ b/Gauntlet.toml
@@ -3060,6 +3060,101 @@ kind = "LintWarning"
 document = "biowdl/tasks:deconstructsigs.wdl"
 message = "[v1::W007::Spacing/Low] missing newline at the end of the file (66:2-66:2)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (10:1-10:77)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (11:1-11:54)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (12:1-12:2)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (13:1-13:77)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (14:1-14:75)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (15:1-15:78)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (16:1-16:73)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (17:1-17:80)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (18:1-18:80)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (19:1-19:12)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (1:1-1:54)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (2:1-2:2)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (3:1-3:79)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (4:1-4:80)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (5:1-5:79)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (6:1-6:76)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (7:1-7:72)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (8:1-8:59)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "biowdl/tasks:deconstructsigs.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (9:1-9:2)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "biowdl/tasks:deepvariant.wdl"
@@ -17145,6 +17240,51 @@ kind = "LintWarning"
 document = "broadinstitute/warp:beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (21:10-21:37)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (3:1-3:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (4:1-4:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:84)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:beta-pipelines/skylab/BuildIndexHisat/BuildIndexHisat3n.9.wdl"
@@ -17580,6 +17720,81 @@ kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (96:6-96:17)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (3:1-3:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (4:1-4:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:92)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:48)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
@@ -17880,6 +18095,81 @@ kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (49:10-49:25)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:79)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (19:1-19:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (20:1-20:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (21:1-21:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (22:1-22:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
@@ -18100,6 +18390,81 @@ kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (40:10-40:25)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (19:1-19:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (20:1-20:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:80)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl"
@@ -19045,6 +19410,166 @@ kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (45:10-45:35)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:70)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:102)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:21)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:31)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:63)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:80)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:67)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (19:1-19:53)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (20:1-20:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (21:1-21:37)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl"
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+
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+
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+
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+
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+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:51)"
+
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+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:3)"
+
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+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl"
@@ -19200,6 +19725,141 @@ kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (94:11-94:37)"
 
+[[concerns]]
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl"
@@ -20390,6 +21050,81 @@ kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (40:10-40:25)"
 
+[[concerns]]
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+
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+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/internal/arrays/imputation/BroadInternalImputation.wdl"
@@ -21240,6 +21975,86 @@ kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (25:10-25:26)"
 
+[[concerns]]
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+
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+
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+
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+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl"
@@ -22010,6 +22825,76 @@ kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl"
 message = "[v1::W007::Spacing/Low] multiple empty lines at the end of file (259:1-260:1)"
 
+[[concerns]]
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+
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+
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+
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 [[concerns]]
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 document = "broadinstitute/warp:pipelines/cemba/build_cemba_references/BuildCembaReferences.wdl"
@@ -22845,6 +23730,11 @@ kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (972:6-972:18)"
 
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+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl"
@@ -24050,6 +24940,66 @@ kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (31:22-31:30)"
 
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+
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+
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+
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+
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 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl"
@@ -24175,6 +25125,21 @@ kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (6:10-6:30)"
 
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 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl"
@@ -24235,6 +25200,16 @@ kind = "LintWarning"
 document = "broadinstitute/warp:pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (31:21-31:39)"
 
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 document = "broadinstitute/warp:pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.wdl"
@@ -25855,6 +26830,21 @@ kind = "LintWarning"
 document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl"
 message = "[v1::W007::Spacing/Low] multiple empty lines at the end of file (235:1-236:1)"
 
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+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterObjects.wdl"
@@ -26050,6 +27040,21 @@ kind = "LintWarning"
 document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (8:10-8:34)"
 
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+
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+
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 document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl"
@@ -27395,6 +28400,11 @@ kind = "LintWarning"
 document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl"
 message = "[v1::W007::Spacing/Low] missing newline at the end of the file (287:2-287:2)"
 
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+
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 document = "broadinstitute/warp:scripts/FilterAFComparisonTable.wdl"
@@ -27685,6 +28695,81 @@ kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (90:10-90:43)"
 
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+
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 document = "broadinstitute/warp:tasks/broad/Alignment.wdl"
@@ -27765,6 +28850,76 @@ kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/Alignment.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (21:6-21:31)"
 
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+
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+
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+
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+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl"
@@ -28250,6 +29405,76 @@ kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (64:6-64:20)"
 
+[[concerns]]
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+
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+
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+
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+
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+
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+
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+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/BamToCram.wdl"
@@ -28430,6 +29655,76 @@ kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (18:6-18:31)"
 
+[[concerns]]
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+
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+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (3:1-3:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (4:1-4:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:94)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:92)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
@@ -28515,6 +29810,86 @@ kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (19:6-19:27)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (25:20-25:46)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (3:1-3:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (4:1-4:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:88)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:55)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:92)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:48)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
@@ -28580,6 +29955,76 @@ kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (21:6-21:32)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (3:1-3:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (4:1-4:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:136)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:92)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl"
@@ -33155,6 +34600,76 @@ kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/Qc.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (93:6-93:39)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (3:1-3:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (4:1-4:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:92)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Qc.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl"
@@ -34410,6 +35925,76 @@ kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (20:10-20:34)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:60)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:86)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl"
@@ -34990,6 +36575,81 @@ kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (290:10-290:16)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (3:1-3:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (4:1-4:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:97)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:53)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:92)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:48)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
@@ -35165,6 +36825,76 @@ kind = "LintWarning"
 document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
 message = "[v1::W007::Spacing/Low] missing newline at the end of the file (301:2-301:2)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (3:1-3:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (4:1-4:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:74)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:92)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/broad/Utilities.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/Attach10xBarcodes.wdl"
@@ -36493,112 +38223,127 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:31)"
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W001::Style/Low] line contains only whitespace (113:1-113:4)"
+message = "[v1::W001::Style/Low] line contains only whitespace (128:1-128:4)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W001::Style/Low] line contains only whitespace (219:1-219:6)"
+message = "[v1::W001::Style/Low] line contains only whitespace (234:1-234:6)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W001::Style/Low] line contains only whitespace (228:1-228:6)"
+message = "[v1::W001::Style/Low] line contains only whitespace (243:1-243:6)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W001::Style/Low] line contains only whitespace (233:1-233:6)"
+message = "[v1::W001::Style/Low] line contains only whitespace (248:1-248:6)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W001::Style/Low] line contains only whitespace (236:1-236:6)"
+message = "[v1::W001::Style/Low] line contains only whitespace (251:1-251:6)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W001::Style/Low] line contains only whitespace (239:1-239:6)"
+message = "[v1::W001::Style/Low] line contains only whitespace (254:1-254:6)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W001::Style/Low] line contains only whitespace (242:1-242:6)"
+message = "[v1::W001::Style/Low] line contains only whitespace (257:1-257:6)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W001::Style/Low] line contains only whitespace (247:1-247:4)"
+message = "[v1::W001::Style/Low] line contains only whitespace (262:1-262:4)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W001::Style/Low] trailing space (100:82)"
+message = "[v1::W001::Style/Low] trailing space (115:82)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W001::Style/Low] trailing space (111:21)"
+message = "[v1::W001::Style/Low] trailing space (126:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W001::Style/Low] trailing space (119:40)"
+message = "[v1::W001::Style/Low] trailing space (134:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W001::Style/Low] trailing space (30:180)"
+message = "[v1::W001::Style/Low] trailing space (33:180)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W001::Style/Low] trailing space (47:73)"
+message = "[v1::W001::Style/Low] trailing space (56:73)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpuPlatform (189:9-189:50)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpuPlatform (204:9-204:50)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nthreads (188:9-188:25)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nthreads (203:9-203:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (123:14-123:20)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (138:14-138:20)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (125:14-125:20)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (140:14-140:20)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (129:6-129:14)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (144:6-144:14)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (184:6-184:19)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (16:12-16:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (186:14-186:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (17:12-17:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (189:16-189:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (18:12-18:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (266:12-266:26)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (199:6-199:19)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (201:14-201:23)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (204:16-204:27)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (281:12-281:26)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -37385,6 +39130,11 @@ kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/accessory_workflows/build_bwa_reference/bwa-mk-index.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (52:16-52:31)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:tasks/skylab/accessory_workflows/build_bwa_reference/bwa-mk-index.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (24:25-24:72)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:tasks/skylab/sample_fastq.14.wdl"
@@ -38165,6 +39915,81 @@ kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyArrays.wdl"
 message = "[v1::W007::Spacing/Low] multiple empty lines at the end of file (78:1-79:1)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (19:1-19:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (20:1-20:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:82)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
@@ -38200,6 +40025,81 @@ kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
 message = "[v1::W007::Spacing/Low] multiple empty lines at the end of file (55:1-56:1)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (19:1-19:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (20:1-20:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:92)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyCramToUnmappedBams.wdl"
@@ -38770,6 +40670,81 @@ kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (41:10-41:29)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (19:1-19:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (20:1-20:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:82)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyImputation.wdl"
@@ -38935,6 +40910,81 @@ kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyImputation.wdl"
 message = "[v1::W007::Spacing/Low] missing newline at the end of the file (177:2-177:2)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (19:1-19:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (20:1-20:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:82)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyImputation.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl"
@@ -39150,6 +41200,81 @@ kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (21:10-21:33)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (19:1-19:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:92)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyMultiSampleSmartSeq2.wdl"
@@ -40105,6 +42230,16 @@ kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (91:10-91:15)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (20:3-20:147)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (62:3-62:14)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl"
@@ -40240,6 +42375,16 @@ kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (6:10-6:49)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (28:3-28:147)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (70:3-70:14)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
@@ -40310,6 +42455,81 @@ kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
 message = "[v1::W007::Spacing/Low] missing newline at the end of the file (96:2-96:2)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:48)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:87)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:84)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (19:1-19:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (20:1-20:62)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:35)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:3)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:86)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "broadinstitute/warp:verification/VerifyValidateChip.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "broadinstitute/warp:verification/VerifyscATAC.wdl"
@@ -47265,6 +49485,26 @@ kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl"
 message = "[v1::W007::Spacing/Low] missing newline at the end of the file (230:2-230:2)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (50:5-50:57)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (51:5-51:37)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (52:5-52:51)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (72:5-72:33)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl"
@@ -47455,6 +49695,16 @@ kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl"
 message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: workflow_type (23:9-23:29)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (28:9-28:88)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (44:9-44:88)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl"
@@ -47770,6 +50020,26 @@ kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl"
 message = "[v1::W007::Spacing/Low] multiple empty lines at the end of file (234:1-235:1)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (51:5-51:57)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (52:5-52:37)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (53:5-53:51)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (73:5-73:33)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl"
@@ -48865,6 +51135,31 @@ kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (928:6-928:18)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (1:1-1:34)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (2:1-2:29)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (3:1-3:85)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (4:1-4:114)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (5:1-5:78)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/diamond/diamond.wdl"
@@ -48920,11 +51215,6 @@ kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/diamond/diamond.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (27:6-27:16)"
 
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/diamond/diamond.wdl"
-message = "[v1::W007::Spacing/Low] missing newline at the end of the file (48:2-48:2)"
-
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/host-genome-generation/run.wdl"
@@ -49013,122 +51303,157 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (35:6-35:24)"
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W001::Style/Low] line contains only whitespace (138:1-138:8)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (193:14-193:38)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W001::Style/Low] line contains only whitespace (72:1-72:4)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (194:14-194:37)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W001::Style/Low] trailing space (418:15)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (195:14-195:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W001::Style/Low] trailing space (88:10)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (196:14-196:34)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (107:19-107:33)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (200:20-200:34)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (10:17-10:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (213:14-213:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (111:6-111:16)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (217:6-217:22)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (130:6-130:16)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (243:6-243:15)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (150:6-150:29)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (267:6-267:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (164:19-164:34)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (26:16-26:48)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (172:6-172:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (271:21-271:42)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (191:6-191:29)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:49)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (196:19-196:34)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (286:14-286:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (216:14-216:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (28:16-28:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (224:6-224:18)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (295:6-295:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (244:6-244:18)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (29:16-29:45)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (263:6-263:26)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (312:6-312:20)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (284:6-284:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (329:6-329:26)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (367:6-367:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (346:6-346:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (430:6-430:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (350:17-350:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (435:16-435:17)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (429:6-429:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (460:19-460:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (434:16-434:17)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (469:6-469:22)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (459:19-459:33)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (473:21-473:42)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (95:14-95:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (49:20-49:25)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (523:6-523:21)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (63:10-63:42)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (64:10-64:43)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (65:10-65:38)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (66:10-66:39)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl"
+message = "[v1::W007::Spacing/Low] missing newline at the end of the file (551:2-551:2)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -49918,22 +52243,22 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (6:12-6:21)"
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (648:9-648:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (652:9-652:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (691:9-691:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (695:9-695:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (740:9-740:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (744:9-744:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (787:9-787:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (791:9-791:32)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -49943,7 +52268,7 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: a
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotated_merged_fa (903:9-903:33)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotated_merged_fa (907:9-907:33)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -49963,37 +52288,37 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: a
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads_fa (596:9-596:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads_fa (598:9-598:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_taxid_annot_fasta (938:9-938:48)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_taxid_annot_fasta (942:9-942:48)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (1235:9-1235:44)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (1239:9-1239:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (1236:9-1236:41)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (1240:9-1240:41)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (1237:9-1237:37)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (1241:9-1241:37)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fasta (1070:9-1070:27)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fasta (1074:9-1074:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (1156:9-1156:38)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (1160:9-1160:38)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50003,52 +52328,57 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: d
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (597:9-597:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (599:9-599:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1029:9-1029:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1033:9-1033:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1109:9-1109:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1113:9-1113:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (734:9-734:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (738:9-738:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (781:9-781:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (785:9-785:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (984:9-984:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (988:9-988:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (598:9-598:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (600:9-600:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1034:9-1034:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_wdl_version (604:9-604:35)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1072:9-1072:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1038:9-1038:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1116:9-1116:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1076:9-1076:31)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1120:9-1120:31)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50058,17 +52388,17 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: d
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1157:9-1157:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1161:9-1161:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1195:9-1195:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1199:9-1199:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1239:9-1239:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1243:9-1243:31)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50123,42 +52453,42 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: d
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (558:9-558:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (559:9-559:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (603:9-603:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (606:9-606:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (649:9-649:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (653:9-653:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (692:9-692:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (696:9-696:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (742:9-742:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (746:9-746:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (789:9-789:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (793:9-793:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (829:9-829:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (833:9-833:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (873:9-873:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (877:9-877:31)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50168,17 +52498,17 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: d
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (907:9-907:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (911:9-911:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (939:9-939:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (943:9-943:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (989:9-989:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (993:9-993:31)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50233,12 +52563,12 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: i
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (825:9-825:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (829:9-829:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: json_files (1194:9-1194:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: json_files (1198:9-1198:31)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50253,47 +52583,47 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: l
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1028:9-1028:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1032:9-1032:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1108:9-1108:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1112:9-1112:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (647:9-647:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (651:9-651:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (690:9-690:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (694:9-694:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (739:9-739:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (743:9-743:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (786:9-786:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (790:9-790:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (906:9-906:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (910:9-910:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (983:9-983:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (987:9-987:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (600:9-600:34)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (602:9-602:34)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50303,18 +52633,23 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: l
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (741:9-741:33)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (745:9-745:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (788:9-788:33)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (792:9-792:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
 message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap2_args (552:9-552:29)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap2_wdl_version (557:9-557:36)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
@@ -50333,122 +52668,122 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: n
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_contig_summary_json (1106:9-1106:36)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_contig_summary_json (1110:9-1110:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1027:9-1027:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1031:9-1031:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1105:9-1105:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1109:9-1109:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (827:9-827:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (831:9-831:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (905:9-905:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (909:9-909:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8 (689:9-689:19)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8 (693:9-693:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1026:9-1026:30)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1030:9-1030:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1104:9-1104:30)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1108:9-1108:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (872:9-872:30)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (876:9-876:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_top_m8 (779:9-779:23)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_top_m8 (783:9-783:23)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_contig_summary_json (1102:9-1102:36)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_contig_summary_json (1106:9-1106:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1101:9-1101:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1105:9-1105:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1233:9-1233:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1237:9-1237:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (826:9-826:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (830:9-830:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (904:9-904:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (908:9-908:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (982:9-982:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (986:9-986:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (1238:9-1238:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (1242:9-1242:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8 (646:9-646:19)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8 (650:9-650:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1100:9-1100:30)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1104:9-1104:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1232:9-1232:30)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1236:9-1236:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (871:9-871:30)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (875:9-875:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (981:9-981:30)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (985:9-985:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (1234:9-1234:23)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (1238:9-1238:23)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (732:9-732:23)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (736:9-736:23)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50458,7 +52793,7 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: p
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pre_alignment_fasta (870:9-870:33)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pre_alignment_fasta (874:9-874:33)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50468,27 +52803,27 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: p
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_contig_sam (1071:9-1071:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_contig_sam (1075:9-1075:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (1025:9-1025:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (1029:9-1029:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (733:9-733:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (737:9-737:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (780:9-780:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (784:9-784:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (980:9-980:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (984:9-984:32)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50508,7 +52843,7 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contigs_tsv (828:9-828:34)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contigs_tsv (832:9-832:34)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50518,17 +52853,17 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (599:9-599:36)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (601:9-601:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (557:9-557:26)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (558:9-558:26)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (602:9-602:26)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (605:9-605:26)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50538,247 +52873,252 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1031:9-1031:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1035:9-1035:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1111:9-1111:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1115:9-1115:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (736:9-736:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (740:9-740:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (783:9-783:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (787:9-787:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (986:9-986:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (990:9-990:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1030:9-1030:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1034:9-1034:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1110:9-1110:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1114:9-1114:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (735:9-735:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (739:9-739:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (782:9-782:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (786:9-786:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (985:9-985:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (989:9-989:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1032:9-1032:40)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1036:9-1036:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1113:9-1113:40)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1117:9-1117:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (737:9-737:40)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (741:9-741:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (784:9-784:40)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (788:9-788:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (987:9-987:40)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (991:9-991:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (1033:9-1033:36)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (1037:9-1037:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (1114:9-1114:36)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (1118:9-1118:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (738:9-738:36)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (742:9-742:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (785:9-785:36)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (789:9-789:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (988:9-988:36)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (992:9-992:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (1288:9-1288:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (1292:9-1292:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (1292:9-1292:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (1296:9-1296:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (1300:9-1300:43)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (1304:9-1304:43)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (1299:9-1299:27)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (1303:9-1303:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (1285:9-1285:36)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (1289:9-1289:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (1268:9-1268:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_wdl_version (1306:9-1306:46)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: guppy_basecaller_setting (1275:9-1275:48)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (1272:9-1272:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_fastq (1272:9-1272:25)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: guppy_basecaller_setting (1279:9-1279:48)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: library_type (1274:9-1274:36)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_fastq (1276:9-1276:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (1287:9-1287:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: library_type (1278:9-1278:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (1291:9-1291:33)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (1291:9-1291:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_args (1296:9-1296:61)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (1295:9-1295:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_db (1295:9-1295:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_args (1300:9-1300:61)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (1284:9-1284:37)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_db (1299:9-1299:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (1297:9-1297:41)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (1288:9-1288:37)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_host_db (1279:9-1279:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (1301:9-1301:41)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_human_db (1280:9-1280:30)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_wdl_version (1307:9-1307:47)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (1293:9-1293:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_host_db (1283:9-1283:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: polishing_iterations (1282:9-1282:37)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_human_db (1284:9-1284:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (1270:9-1270:26)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (1297:9-1297:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: subsample_depth (1277:9-1277:38)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: polishing_iterations (1286:9-1286:37)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (1289:9-1289:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (1274:9-1274:26)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_whitelist (1290:9-1290:113)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: subsample_depth (1281:9-1281:38)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (1302:9-1302:47)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (1293:9-1293:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (1303:9-1303:44)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_whitelist (1294:9-1294:113)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1023:6-1023:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (1309:9-1309:47)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1026:14-1026:30)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (1310:9-1310:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1068:6-1068:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1027:6-1027:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1098:6-1098:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1030:14-1030:30)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1072:6-1072:27)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50788,7 +53128,7 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (109:6-109:19)"
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1100:14-1100:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1102:6-1102:30)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50798,77 +53138,87 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (1104:14-1104:30
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1143:14-1143:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1108:14-1108:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1144:14-1144:36)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1147:14-1147:23)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1154:6-1154:24)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1148:14-1148:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1192:6-1192:17)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1158:6-1158:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1230:6-1230:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1196:6-1196:17)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1232:14-1232:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1234:6-1234:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1234:14-1234:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1236:14-1236:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1270:17-1270:26)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1238:14-1238:23)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1284:15-1284:37)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1274:17-1274:26)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1288:14-1288:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1288:15-1288:37)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1295:17-1295:28)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1292:14-1292:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1296:16-1296:29)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1299:17-1299:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1297:16-1297:31)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1300:16-1300:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1616:14-1616:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1301:16-1301:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (1618:14-1618:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1307:16-1307:36)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1625:14-1625:23)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (1627:14-1627:23)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50938,17 +53288,22 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (554:15-554:35)"
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (557:17-557:26)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (557:16-557:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (586:14-586:19)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (558:17-558:26)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (594:6-594:20)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (588:14-588:19)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (596:6-596:20)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -50958,132 +53313,132 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (5:6-5:22)"
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (602:17-602:26)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (605:17-605:26)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (635:14-635:19)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (639:14-639:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (644:6-644:19)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (648:6-648:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (646:14-646:19)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (650:14-650:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (648:14-648:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (652:14-652:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (678:14-678:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (682:14-682:23)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (687:6-687:19)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (691:6-691:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (689:14-689:19)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (693:14-693:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (691:14-691:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (695:14-695:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (721:14-721:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (725:14-725:23)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (730:6-730:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (734:6-734:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (732:14-732:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (736:14-736:23)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (740:14-740:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (744:14-744:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (767:14-767:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (771:14-771:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (777:6-777:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (781:6-781:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (779:14-779:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (783:14-783:23)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (787:14-787:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (791:14-791:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (814:14-814:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (818:14-818:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (823:6-823:19)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (827:6-827:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (868:6-868:28)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (872:6-872:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (871:14-871:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (875:14-875:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (872:14-872:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (876:14-876:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (901:6-901:24)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (905:6-905:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (936:6-936:26)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (940:6-940:26)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (978:6-978:24)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (982:6-982:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (981:14-981:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (985:14-985:30)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -51438,17 +53793,17 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (394:6-394:23)"
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (162:5-162:40)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (126:5-126:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (163:5-163:37)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (127:5-127:37)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (164:5-164:33)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (128:5-128:33)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -51460,11 +53815,6 @@ kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
 message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (157:5-157:27)"
 
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (193:5-193:27)"
-
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
@@ -51483,27 +53833,17 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: d
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (197:5-197:32)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (123:5-123:23)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (195:5-195:23)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (161:5-161:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_ext (124:5-124:20)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (159:5-159:23)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8_gsnap_deduped_m8 (165:5-165:35)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8_gsnap_deduped_m8 (129:5-129:35)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -51518,7 +53858,7 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: l
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nonhost_fasta_refined_taxid_annot_fasta (196:5-196:49)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nonhost_fasta_refined_taxid_annot_fasta (160:5-160:49)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -51528,7 +53868,7 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: n
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (166:5-166:20)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (130:5-130:20)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -51538,27 +53878,17 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: n
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_blast_top_m8 (161:5-161:45)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_blast_top_m8 (125:5-125:45)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_hitsummary2_tab (160:5-160:48)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_hitsummary2_tab (124:5-124:48)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_reassigned_m8 (159:5-159:46)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: resist_genome_bed (126:5-126:27)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: resist_genome_db (125:5-125:26)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_reassigned_m8 (123:5-123:46)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -51570,11 +53900,6 @@ kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
 message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (158:5-158:21)"
 
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (194:5-194:21)"
-
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
@@ -51678,132 +54003,132 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: t
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (198:5-198:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (162:5-162:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_coverage_json (234:5-234:40)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_coverage_json (198:5-198:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_stats_json (235:5-235:37)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_stats_json (199:5-199:37)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contigs_fasta (236:5-236:33)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contigs_fasta (200:5-200:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (225:5-225:27)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (189:5-189:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_clusters_csv (240:5-240:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_clusters_csv (204:5-204:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (237:5-237:18)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (201:5-201:18)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (238:5-238:19)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (202:5-202:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: file_ext (241:5-241:30)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: file_ext (205:5-205:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_m8_gsnap_deduped_m8 (230:5-230:35)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_m8_gsnap_deduped_m8 (194:5-194:35)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (245:5-245:90)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (209:5-209:90)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nonhost_fasta_refined_taxid_annot_fasta (239:5-239:49)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nonhost_fasta_refined_taxid_annot_fasta (203:5-203:49)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_db (242:5-242:76)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_db (206:5-206:76)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (244:5-244:89)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (208:5-208:89)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (243:5-243:87)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (207:5-207:87)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_blast_top_m8 (233:5-233:45)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_blast_top_m8 (197:5-197:45)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_hitsummary2_tab (232:5-232:48)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_hitsummary2_tab (196:5-196:48)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_reassigned_m8 (231:5-231:46)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_reassigned_m8 (195:5-195:46)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_bed (247:5-247:83)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_bed (211:5-211:83)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_db (246:5-246:80)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_db (210:5-210:80)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (226:5-226:21)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (190:5-190:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_annotated_merged_fa (227:5-227:44)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_annotated_merged_fa (191:5-191:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_gsnap_hitsummary_tab (228:5-228:45)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_gsnap_hitsummary_tab (192:5-192:45)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_rapsearch2_hitsummary_tab (229:5-229:50)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_rapsearch2_hitsummary_tab (193:5-193:50)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (248:5-248:40)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (212:5-212:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (119:6-119:14)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (119:6-119:25)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -51813,148 +54138,88 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (122:12-122:21)"
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (143:10-143:46)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (144:10-144:50)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (147:10-147:41)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (155:6-155:25)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (158:12-158:21)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (159:10-159:46)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (160:10-160:48)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (161:10-161:45)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (165:10-165:35)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (191:6-191:18)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (123:10-123:46)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (194:12-194:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (124:10-124:48)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (214:10-214:26)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (125:10-125:45)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (215:11-215:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (129:10-129:35)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (226:12-226:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (155:6-155:18)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (229:10-229:50)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (230:10-230:35)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (158:12-158:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (231:10-231:46)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (178:10-178:26)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (232:10-232:48)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (179:11-179:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (233:10-233:45)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (190:12-190:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (343:10-343:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (193:10-193:50)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (344:10-344:56)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (194:10-194:35)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (345:10-345:60)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (195:10-195:46)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (346:10-346:45)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (196:10-196:48)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (347:10-347:43)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (197:10-197:45)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (348:10-348:51)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (299:10-299:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (349:11-349:26)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (300:11-300:45)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (34:6-34:26)"
 
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (352:10-352:44)"
-
-[[concerns]]
-kind = "LintWarning"
-document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (353:11-353:45)"
-
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl"
@@ -52830,6 +55095,31 @@ kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (953:12-953:21)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (710:1-710:100)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (711:1-711:98)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (712:1-712:99)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (713:1-713:96)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl"
+message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (714:1-714:100)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl"
@@ -52883,57 +55173,57 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (21:16-21:25)"
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W001::Style/Low] trailing space (123:28)"
+message = "[v1::W001::Style/Low] trailing space (125:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W001::Style/Low] trailing space (131:28)"
+message = "[v1::W001::Style/Low] trailing space (134:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W001::Style/Low] trailing space (132:48)"
+message = "[v1::W001::Style/Low] trailing space (135:48)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W001::Style/Low] trailing space (137:18)"
+message = "[v1::W001::Style/Low] trailing space (140:18)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W001::Style/Low] trailing space (171:22)"
+message = "[v1::W001::Style/Low] trailing space (175:22)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W001::Style/Low] trailing space (227:22)"
+message = "[v1::W001::Style/Low] trailing space (231:22)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W001::Style/Low] trailing space (307:35)"
+message = "[v1::W001::Style/Low] trailing space (313:35)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W001::Style/Low] trailing space (308:19)"
+message = "[v1::W001::Style/Low] trailing space (314:19)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W001::Style/Low] trailing space (318:28)"
+message = "[v1::W001::Style/Low] trailing space (325:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W001::Style/Low] trailing space (332:11)"
+message = "[v1::W001::Style/Low] trailing space (339:11)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W001::Style/Low] trailing space (342:28)"
+message = "[v1::W001::Style/Low] trailing space (350:28)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -52948,22 +55238,22 @@ message = "[v1::W001::Style/Low] trailing space (78:35)"
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (169:9-169:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (173:9-173:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (225:9-225:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (229:9-229:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (174:9-174:33)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (178:9-178:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (230:9-230:33)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (234:9-234:33)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -52978,7 +55268,7 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: c
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (122:9-122:23)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (124:9-124:23)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -52988,32 +55278,37 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: d
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (168:9-168:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (172:9-172:29)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (228:9-228:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (224:9-224:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (125:9-125:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (123:9-123:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_wdl_version (129:9-129:35)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (119:9-119:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (121:9-121:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (173:9-173:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (177:9-177:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (229:9-229:31)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (233:9-233:31)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -53033,12 +55328,12 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: d
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (170:9-170:36)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (174:9-174:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (226:9-226:36)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (230:9-230:36)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -53048,7 +55343,7 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: d
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastas (121:9-121:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastas (123:9-123:28)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -53083,17 +55378,17 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: h
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (166:9-166:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (170:9-170:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (222:9-222:24)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (226:9-226:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (125:9-125:34)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (127:9-127:34)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -53103,22 +55398,22 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: l
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (165:9-165:21)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (169:9-169:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (221:9-221:21)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (225:9-225:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (172:9-172:33)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (176:9-176:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (228:9-228:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (232:9-232:32)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -53128,17 +55423,22 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (126:9-126:22)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap2_wdl_version (80:9-80:36)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (128:9-128:22)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (171:9-171:22)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (175:9-175:22)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (227:9-227:22)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (231:9-231:22)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -53168,7 +55468,7 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (124:9-124:37)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (126:9-126:37)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -53178,17 +55478,17 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (120:9-120:25)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (122:9-122:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (175:9-175:25)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (179:9-179:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (231:9-231:25)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (235:9-235:25)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -53208,257 +55508,272 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (167:9-167:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (171:9-171:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (223:9-223:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (227:9-227:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (286:5-286:105)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (290:5-290:105)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: alignment_scalability (293:5-293:42)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: alignment_scalability (297:5-297:42)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: czid_dedup_out_duplicate_clusters_csv (283:5-283:47)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: czid_dedup_out_duplicate_clusters_csv (287:5-287:47)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (290:5-290:101)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (294:5-294:101)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (302:5-302:42)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (306:5-306:42)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (300:5-300:79)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (304:5-304:79)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (296:5-296:32)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (300:5-300:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_prefix (304:5-304:41)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_prefix (308:5-308:41)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (277:5-277:27)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_wdl_version (310:5-310:42)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_cluster_sizes_tsv (282:5-282:37)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (281:5-281:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_1_fa (279:5-279:43)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_cluster_sizes_tsv (286:5-286:37)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_2_fa (280:5-280:44)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_1_fa (283:5-283:43)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_merged_fa (281:5-281:49)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_2_fa (284:5-284:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_dir_suffix (288:5-288:44)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_merged_fa (285:5-285:49)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_version (284:5-284:40)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_dir_suffix (292:5-292:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (285:5-285:90)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_version (288:5-288:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_genome_name (297:5-297:36)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (289:5-289:90)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_index (294:5-294:28)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_genome_name (301:5-301:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_rapsearch2_index (298:5-298:33)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_index (298:5-298:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (289:5-289:29)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_rapsearch2_index (302:5-302:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_args (301:5-301:52)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (293:5-293:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_db (299:5-299:94)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_args (305:5-305:52)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (295:5-295:33)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_db (303:5-303:94)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (303:5-303:37)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (299:5-299:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (278:5-278:21)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (307:5-307:37)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (287:5-287:97)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_wdl_version (309:5-309:43)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (291:5-291:43)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (282:5-282:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (292:5-292:40)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (291:5-291:97)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (109:14-109:20)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (295:5-295:43)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (117:6-117:30)"
+message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (296:5-296:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (120:16-120:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (111:14-111:20)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (154:14-154:20)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (119:6-119:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (163:6-163:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (122:16-122:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (165:14-165:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (158:14-158:20)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (169:14-169:29)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (167:6-167:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (175:16-175:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (169:14-169:21)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (173:14-173:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (209:14-209:28)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (179:16-179:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (219:6-219:24)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (213:14-213:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (221:14-221:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (223:6-223:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (225:14-225:29)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (225:14-225:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (231:16-231:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (229:14-229:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (264:14-264:28)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (235:16-235:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (278:12-278:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (268:14-268:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (286:10-286:28)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (282:12-282:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (295:11-295:33)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (290:10-290:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (298:11-298:33)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (299:11-299:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (299:12-299:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (302:11-302:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (301:12-301:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (303:12-303:23)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (303:12-303:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (305:12-305:25)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (307:12-307:27)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (309:12-309:32)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -53483,47 +55798,47 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (37:10-37:26)"
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (383:10-383:28)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (391:10-391:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (384:10-384:36)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (392:10-392:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (387:11-387:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (395:11-395:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (389:10-389:38)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (397:10-397:38)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (390:10-390:46)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (398:10-398:46)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (391:10-391:50)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (399:10-399:50)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (392:10-392:56)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (394:11-394:31)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (400:10-400:56)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:24)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (402:11-402:31)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -53570,6 +55885,11 @@ kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (78:15-78:35)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (80:16-80:36)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl"
@@ -54785,6 +57105,91 @@ kind = "LintWarning"
 document = "stjudecloud/workflows:data_structures/flag_filter.wdl"
 message = "[v1::W006::Naming/Low] identifier must be snake case (71:6-71:45)"
 
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (143:6-143:24)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (32:12-32:14)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (33:13-33:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (34:13-34:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (35:13-35:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (36:13-36:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (37:13-37:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (38:13-38:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (39:13-39:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (40:13-40:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (41:10-41:12)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (42:13-42:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (43:13-43:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (44:13-44:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (45:13-45:15)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (48:6-48:25)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:data_structures/read_group.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (96:6-96:20)"
+
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/cellranger.wdl"
@@ -54813,52 +57218,82 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (87:14-87:25)"
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/fq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (141:11-141:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (139:11-139:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/fq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (142:11-142:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (140:11-140:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/fq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (151:12-151:18)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (149:12-149:18)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/fq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (152:12-152:18)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (150:12-150:18)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/fq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (168:14-168:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (166:14-166:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/fq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (169:15-169:31)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (167:15-167:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/fq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (73:11-73:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (71:11-71:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/fq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (74:11-74:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (72:11-72:21)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:tools/gatk4.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (107:14-107:23)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:tools/gatk4.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (108:14-108:29)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:tools/gatk4.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (109:21-109:44)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:tools/gatk4.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (249:14-249:23)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:tools/gatk4.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (250:14-250:29)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:tools/gatk4.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (62:14-62:35)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/kraken2.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (349:11-349:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (347:11-347:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/kraken2.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (350:11-350:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (348:11-348:21)"
 
 [[concerns]]
 kind = "LintWarning"
@@ -54868,712 +57303,742 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (30:11-30:21)"
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/md5sum.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (38:14-38:20)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (36:14-36:20)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/picard.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (119:15-119:39)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (121:15-121:39)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/picard.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (325:14-325:28)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (327:14-327:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/picard.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (420:14-420:28)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (422:14-422:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/picard.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (481:14-481:29)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (483:14-483:29)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:tools/sambamba.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (2:1-2:2)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:tools/sambamba.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (3:1-3:31)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:tools/sambamba.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (4:1-4:50)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (480:20-480:47)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (478:20-478:47)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (481:19-481:41)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (479:19-479:41)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (487:19-487:44)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (485:19-485:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (493:19-493:43)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (491:19-491:43)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (499:19-499:46)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (497:19-497:46)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (505:19-505:44)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (503:19-503:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (511:30-511:46)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (509:30-509:46)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (512:28-512:44)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (510:28-510:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (513:27-513:44)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (511:27-511:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (514:24-514:36)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (512:24-512:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (515:24-515:48)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (513:24-513:48)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (516:24-516:36)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (514:24-514:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (517:16-517:33)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (515:16-515:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (518:16-518:31)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (516:16-516:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (519:16-519:33)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (517:16-517:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (520:16-520:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (518:16-518:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (521:16-521:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (519:16-519:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (522:16-522:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (520:16-520:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (523:16-523:28)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (521:16-521:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (524:16-524:26)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (522:16-522:26)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (525:16-525:29)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (523:16-523:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (526:16-526:37)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (524:16-524:37)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (527:16-527:38)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (525:16-525:38)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (528:16-528:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (526:16-526:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (529:16-529:29)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (527:16-527:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (530:16-530:44)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (528:16-528:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (531:16-531:35)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (529:16-529:35)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (532:16-532:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (530:16-530:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (533:16-533:26)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (531:16-531:26)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (534:16-534:37)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (532:16-532:37)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (535:16-535:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (533:16-533:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (537:15-537:41)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (535:15-535:41)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (538:15-538:45)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (536:15-536:45)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (539:15-539:41)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (537:15-537:41)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (540:15-540:42)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (538:15-538:42)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (541:15-541:42)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (539:15-539:42)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (542:15-542:43)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (53:16-53:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (543:15-543:47)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (540:15-540:43)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (544:15-544:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (541:15-541:47)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (545:13-545:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (542:15-542:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (546:13-546:22)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (543:13-543:23)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (547:13-547:26)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (544:13-544:22)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (548:13-548:33)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (545:13-545:26)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (549:13-549:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (546:13-546:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (550:13-550:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (547:13-547:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (551:13-551:31)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (548:13-548:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (552:13-552:31)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (549:13-549:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (553:13-553:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (54:16-54:34)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (554:13-554:29)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (550:13-550:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (555:13-555:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (551:13-551:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (556:13-556:26)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (552:13-552:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (557:13-557:40)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (553:13-553:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (558:13-558:34)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (554:13-554:26)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (559:13-559:34)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (555:13-555:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (55:16-55:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (556:13-556:34)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (560:13-560:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (557:13-557:34)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (561:13-561:31)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (558:13-558:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (562:13-562:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (559:13-559:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (563:13-563:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (55:16-55:46)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (564:13-564:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (560:13-560:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (565:13-565:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (561:13-561:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (566:13-566:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (562:13-562:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (567:13-567:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (563:13-563:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (568:13-568:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (564:13-564:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (569:13-569:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (565:13-565:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (56:16-56:34)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (566:13-566:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (570:13-570:31)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (567:13-567:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (571:13-571:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (568:13-568:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (572:13-572:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (569:13-569:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (573:13-573:29)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (56:16-56:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (574:13-574:28)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (570:13-570:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (575:13-575:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (571:13-571:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (576:13-576:34)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (572:13-572:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (577:13-577:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (573:13-573:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (578:13-578:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (574:13-574:34)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (579:13-579:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (575:13-575:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (57:16-57:46)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (576:13-576:23)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (580:13-580:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (577:13-577:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (581:13-581:29)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (578:13-578:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (582:13-582:31)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (579:13-579:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (583:13-583:33)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (57:16-57:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (584:13-584:36)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (580:13-580:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (585:13-585:36)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (581:13-581:33)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (586:13-586:42)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (582:13-582:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (587:13-587:40)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (583:13-583:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (588:13-588:31)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (584:13-584:42)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (589:13-589:34)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (585:13-585:40)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (58:16-58:40)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (586:13-586:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (590:13-590:24)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (587:13-587:34)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (591:13-591:31)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (588:13-588:24)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (592:13-592:26)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (589:13-589:31)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (593:13-593:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (58:16-58:44)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (594:13-594:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (590:13-590:26)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (595:13-595:29)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (591:13-591:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (596:13-596:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (592:13-592:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (597:13-597:37)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (593:13-593:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (598:13-598:36)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (594:13-594:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (599:13-599:34)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (595:13-595:37)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (59:16-59:44)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (596:13-596:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (600:13-600:36)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (597:13-597:34)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (601:13-601:29)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (598:13-598:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (602:13-602:35)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (599:13-599:29)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (603:13-603:36)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (600:13-600:35)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (604:13-604:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (601:13-601:36)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (60:16-60:44)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (602:13-602:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (62:13-62:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (60:13-60:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (63:13-63:32)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (61:13-61:32)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (64:13-64:28)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (62:13-62:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (65:13-65:34)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (63:13-63:34)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (66:13-66:25)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (64:13-64:25)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (818:9-818:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (816:9-816:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (819:9-819:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (817:9-817:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/star.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (820:9-820:30)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (818:9-818:30)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/util.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (26:17-26:23)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (24:17-24:23)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:tools/util.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (415:14-415:21)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (413:14-413:21)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:workflows/general/bam-to-fastqs.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (51:21-51:27)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (49:21-49:27)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:workflows/general/bam-to-fastqs.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (52:22-52:28)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (50:22-50:28)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:workflows/qc/quality-check-standard.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (572:11-572:35)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (570:11-570:35)"
 
 [[concerns]]
 kind = "LintWarning"
 document = "stjudecloud/workflows:workflows/reference/bwa-db-build.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (28:17-28:33)"
+message = "[v1::W006::Naming/Low] identifier must be snake case (26:17-26:33)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/reference/make-qc-reference.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (127:14-127:21)"
+document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (103:15-103:24)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/reference/star-db-build.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (35:17-35:33)"
+document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (104:15-104:30)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/reference/star-db-build.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (36:17-36:24)"
+document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (106:21-106:30)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (41:16-41:32)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (42:16-42:29)"
+
+[[concerns]]
+kind = "LintWarning"
+document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (43:16-43:30)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (182:12-182:14)"
+document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (44:17-44:36)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (183:13-183:15)"
+document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (45:17-45:37)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (184:13-184:15)"
+document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (46:23-46:36)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (185:13-185:15)"
+document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (47:23-47:37)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (186:13-186:15)"
+document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl"
+message = "[v1::W007::Spacing/Low] missing newline at the end of the file (108:2-108:2)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (187:13-187:15)"
+document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (1:1-1:31)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (188:13-188:15)"
+document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (2:1-2:50)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (189:13-189:15)"
+document = "stjudecloud/workflows:workflows/reference/make-qc-reference.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (125:14-125:21)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (190:13-190:15)"
+document = "stjudecloud/workflows:workflows/reference/star-db-build.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (33:17-33:33)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (191:10-191:12)"
+document = "stjudecloud/workflows:workflows/reference/star-db-build.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (34:17-34:24)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (192:13-192:15)"
+document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-variant-calling.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (44:14-44:23)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (193:13-193:15)"
+document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-variant-calling.wdl"
+message = "[v1::W006::Naming/Low] identifier must be snake case (45:14-45:29)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (194:13-194:15)"
+document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-variant-calling.wdl"
+message = "[v1::W007::Spacing/Low] multiple empty lines at the end of file (126:1-127:1)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (195:13-195:15)"
+document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-variant-calling.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (1:1-1:31)"
 
 [[concerns]]
 kind = "LintWarning"
-document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl"
-message = "[v1::W006::Naming/Low] identifier must be snake case (198:6-198:25)"
+document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-variant-calling.wdl"
+message = "[v1::W010::Style/Low] preamble comment without a double pound sign (2:1-2:50)"
 
 [[concerns]]
 kind = "LintWarning"
diff --git a/RULES.md b/RULES.md
index b27959bd..afecc6b2 100644
--- a/RULES.md
+++ b/RULES.md
@@ -24,6 +24,7 @@ repository. Note that the information may be out of sync with released packages.
 | `missing_runtime_block`   | `v1::W005` | Completeness | [`wdl-grammar`][wdl-grammar-lints] |
 | `snake_case`              | `v1::W006` | Naming       | [`wdl-grammar`][wdl-grammar-lints] |
 | `newline_eof`             | `v1::W007` | Spacing      | [`wdl-grammar`][wdl-grammar-lints] |
+| `preamble_comment`        | `v1::W010` | Style        | [`wdl-grammar`][wdl-grammar-lints] |
 
 [wdl-ast-lints]: https://docs.rs/wdl-ast/latest/wdl_ast/v1/index.html#lint-rules
 [wdl-ast-validation]: https://docs.rs/wdl-ast/latest/wdl_ast/v1/index.html#validation-rules
diff --git a/wdl-grammar/CHANGELOG.md b/wdl-grammar/CHANGELOG.md
index ff654564..c5c1d019 100644
--- a/wdl-grammar/CHANGELOG.md
+++ b/wdl-grammar/CHANGELOG.md
@@ -14,6 +14,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * Adds the `snake_case` rule that ensures all tasks, workflows, and variables
   are snakecase (#13, contributed by @simojoe).
 * Adds the `newline_eof` rule for tasks (#18, contributed by @simojoe).
+* Adds the `preamble_comment` rule for preamble comments formatting (contributed
+  by @simojoe).
 
 ## 0.2.0 - 12-17-2023
 
diff --git a/wdl-grammar/src/v1.rs b/wdl-grammar/src/v1.rs
index ecfbd2e0..30709687 100644
--- a/wdl-grammar/src/v1.rs
+++ b/wdl-grammar/src/v1.rs
@@ -23,6 +23,7 @@
 //! | `missing_runtime_block` | `v1::W005` | Completeness | [Link](lint::MissingRuntimeBlock) |
 //! | `snake_case`            | `v1::W006` | Naming       | [Link](lint::SnakeCase)           |
 //! | `newline_eof`           | `v1::W007` | Spacing      | [Link](lint::NewlineEOF)          |
+//! | `preamble_comment`      | `v1::W010` | Style        | [Link](lint::PreambleComment)     |
 
 use pest::iterators::Pair;
 use pest::Parser as _;
diff --git a/wdl-grammar/src/v1/lint.rs b/wdl-grammar/src/v1/lint.rs
index c8b3c666..de07d32e 100644
--- a/wdl-grammar/src/v1/lint.rs
+++ b/wdl-grammar/src/v1/lint.rs
@@ -6,6 +6,7 @@ mod missing_runtime_block;
 mod mixed_indentation;
 mod newline_eof;
 mod no_curly_commands;
+mod preamble_comment;
 mod snake_case;
 mod whitespace;
 
@@ -13,6 +14,7 @@ pub use missing_runtime_block::MissingRuntimeBlock;
 pub use mixed_indentation::MixedIndentation;
 pub use newline_eof::NewlineEOF;
 pub use no_curly_commands::NoCurlyCommands;
+pub use preamble_comment::PreambleComment;
 pub use snake_case::SnakeCase;
 pub use whitespace::Whitespace;
 
@@ -31,5 +33,7 @@ pub fn rules<'a>() -> Vec<Box<dyn wdl_core::concern::lint::Rule<&'a Pair<'a, cra
         Box::new(SnakeCase),
         // v1::W007
         Box::new(NewlineEOF),
+        // v1::W010
+        Box::new(PreambleComment),
     ]
 }
diff --git a/wdl-grammar/src/v1/lint/preamble_comment.rs b/wdl-grammar/src/v1/lint/preamble_comment.rs
new file mode 100644
index 00000000..5c8c023f
--- /dev/null
+++ b/wdl-grammar/src/v1/lint/preamble_comment.rs
@@ -0,0 +1,181 @@
+//! Preamble comments are full line comments starting with a double pound sign
+//! and must occur before the version declaration
+
+use std::collections::VecDeque;
+
+use nonempty::NonEmpty;
+use pest::iterators::Pair;
+use wdl_core::concern::code;
+use wdl_core::concern::lint;
+use wdl_core::concern::lint::Group;
+use wdl_core::concern::lint::Rule;
+use wdl_core::concern::Code;
+use wdl_core::file::Location;
+use wdl_core::Version;
+
+use crate::v1;
+
+/// Detects preamble comments declaration
+#[derive(Debug)]
+pub struct PreambleComment;
+
+impl<'a> PreambleComment {
+    /// Creates a warning for preamble comments without double pound sign
+    fn missing_double_pound_sign(&self, location: Location) -> lint::Warning
+    where
+        Self: Rule<&'a Pair<'a, v1::Rule>>,
+    {
+        lint::warning::Builder::default()
+            .code(self.code())
+            .level(lint::Level::Low)
+            .group(self.group())
+            .subject("preamble comment without a double pound sign")
+            .body(
+                "Preamble comments are full line comments before the version declaration and they \
+                 start with a double pound sign.",
+            )
+            .push_location(location)
+            .fix("Add a pound sign at the start of the line.")
+            .try_build()
+            .unwrap()
+    }
+
+    /// Creates a warning for preamble comments after version declaration
+    fn preamble_comment_after_version(&self, location: Location) -> lint::Warning
+    where
+        Self: Rule<&'a Pair<'a, v1::Rule>>,
+    {
+        lint::warning::Builder::default()
+            .code(self.code())
+            .level(lint::Level::Low)
+            .group(self.group())
+            .subject("double pound signs are reserved for preamble comments")
+            .body(
+                "Only full line comments before the version declaration should start with a \
+                 double pound sign.",
+            )
+            .push_location(location)
+            .fix("Remove a pound sign at the start of the comment.")
+            .try_build()
+            .unwrap()
+    }
+}
+
+impl<'a> Rule<&Pair<'a, v1::Rule>> for PreambleComment {
+    fn code(&self) -> Code {
+        // SAFETY: this manually crafted to unwrap successfully every time.
+        Code::try_new(code::Kind::Warning, Version::V1, 10).unwrap()
+    }
+
+    fn group(&self) -> lint::Group {
+        Group::Style
+    }
+
+    fn check(&self, tree: &Pair<'a, v1::Rule>) -> lint::Result {
+        let mut warnings = VecDeque::new();
+
+        let mut is_preamble = true;
+
+        for node in tree.clone().into_inner().flatten() {
+            match node.as_rule() {
+                v1::Rule::version => {
+                    is_preamble = false;
+                }
+                v1::Rule::COMMENT => {
+                    // Catches missing double pound sign
+                    if is_preamble & !node.as_str().starts_with("##") {
+                        let location =
+                            Location::try_from(node.as_span()).map_err(lint::Error::Location)?;
+                        warnings.push_back(self.missing_double_pound_sign(location));
+                    }
+
+                    // Catches preamble comment after version declaration
+                    if !is_preamble & node.as_str().starts_with("##") {
+                        let location =
+                            Location::try_from(node.as_span()).map_err(lint::Error::Location)?;
+                        warnings.push_back(self.preamble_comment_after_version(location));
+                    }
+                }
+                _ => {}
+            }
+        }
+
+        match warnings.pop_front() {
+            Some(front) => {
+                let mut results = NonEmpty::new(front);
+                results.extend(warnings);
+                Ok(Some(results))
+            }
+            None => Ok(None),
+        }
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use pest::Parser as _;
+    use wdl_core::concern::lint::Rule as _;
+
+    use super::*;
+    use crate::v1::parse::Parser;
+    use crate::v1::Rule;
+
+    #[test]
+    fn it_catches_badly_formatted_preamble_comment() -> Result<(), Box<dyn std::error::Error>> {
+        let tree = Parser::parse(
+            Rule::document,
+            r#"# a comment
+version 1.0
+"#,
+        )?
+        .next()
+        .unwrap();
+
+        let warnings = PreambleComment.check(&tree)?.unwrap();
+        assert_eq!(warnings.len(), 1);
+        assert_eq!(
+            warnings.first().to_string(),
+            "[v1::W010::Style/Low] preamble comment without a double pound sign (1:1-1:12)"
+        );
+        Ok(())
+    }
+
+    #[test]
+    fn it_catches_preamble_comment_after_version() -> Result<(), Box<dyn std::error::Error>> {
+        let tree = Parser::parse(
+            Rule::document,
+            r#"## a comment
+version 1.0
+
+## a wrong comment
+"#,
+        )?
+        .next()
+        .unwrap();
+
+        let warnings = PreambleComment.check(&tree)?.unwrap();
+        assert_eq!(warnings.len(), 1);
+        assert_eq!(
+            warnings.first().to_string(),
+            "[v1::W010::Style/Low] double pound signs are reserved for preamble comments \
+             (4:1-4:19)"
+        );
+        Ok(())
+    }
+
+    #[test]
+    fn it_ignores_a_properly_formatted_preamble_comment() -> Result<(), Box<dyn std::error::Error>>
+    {
+        let tree = Parser::parse(
+            Rule::document,
+            r#"## a comment
+version 1.0
+"#,
+        )?
+        .next()
+        .unwrap();
+        let warnings = PreambleComment.check(&tree)?;
+        assert!(warnings.is_none());
+        Ok(())
+    }
+}