From d0231f92502644d36b4352e05110e6f7908f62d9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Wed, 8 May 2024 21:49:33 -0400 Subject: [PATCH 1/6] feat: adding header_comment lint rule --- Gauntlet.toml | 3577 ++++++++++++++++++++- RULES.md | 1 + wdl-grammar/CHANGELOG.md | 2 + wdl-grammar/src/v1.rs | 1 + wdl-grammar/src/v1/lint.rs | 4 + wdl-grammar/src/v1/lint/header_comment.rs | 178 + 6 files changed, 3727 insertions(+), 36 deletions(-) create mode 100644 wdl-grammar/src/v1/lint/header_comment.rs diff --git a/Gauntlet.toml b/Gauntlet.toml index 240b17c4..d334a06c 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] header comments without a double pound sign (10:1-10:77)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (11:1-11:54)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (12:1-12:2)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (13:1-13:77)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (14:1-14:75)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (15:1-15:78)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (16:1-16:73)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (17:1-17:80)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (18:1-18:80)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (19:1-19:12)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (1:1-1:54)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (2:1-2:2)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (3:1-3:79)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (4:1-4:80)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (5:1-5:79)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (6:1-6:76)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (7:1-7:72)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (8:1-8:59)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W010::Style/Low] header comments 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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (10:1-10:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:92)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (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 sign are reserved for header comment (10:1-10:79)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (21:1-21:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (22:1-22:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (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 sign are reserved for header comment (10:1-10:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:80)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (21:1-21:37)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (22:1-22:47)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (23:1-23:52)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (24:1-24:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (25:1-25:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (26:1-26:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (27:1-27:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (28:1-28:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (29:1-29:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (30:1-30:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (31:1-31:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (32:1-32:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (33:1-33:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (34:1-34:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:51)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:112)" + [[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]] +kind = "LintWarning" +document = 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= "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:53)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:37)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:47)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:52)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (21:1-21:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (22:1-22:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (23:1-23:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (24:1-24:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = 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"LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:47)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:31)" + [[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]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:62)" + +[[concerns]] +kind = "LintWarning" +document = 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"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]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:56)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:140)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:153)" + +[[concerns]] +kind = "LintWarning" +document = 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(17:1-17:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (21:1-21:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (22:1-22:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (23:1-23:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" + [[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]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:66)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" + [[concerns]] kind = "LintWarning" 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)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (333:5-333:13)" + [[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)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:66)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (21:1-21:63)" + [[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)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (134:3-134:44)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (149:3-149:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (80:3-80:32)" + [[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)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (129:3-129:44)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (145:3-145:26)" + [[concerns]] kind = "LintWarning" 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)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (109:3-109:83)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (190:3-190:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (43:3-43:70)" + [[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)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (120:3-120:79)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (204:3-204:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (40:3-40:70)" + [[concerns]] kind = "LintWarning" 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)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (40:31-40:59)" + [[concerns]] kind = "LintWarning" 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)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (2:1-2:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:97)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:53)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:92)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" + [[concerns]] kind = "LintWarning" 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)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:93)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:92)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" + [[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]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:103)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:92)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" + [[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]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:94)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:92)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (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 sign are reserved for header comment (10:1-10:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (25:20-25:46)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:88)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:55)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:92)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (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 sign are reserved for header comment (10:1-10:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:136)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:92)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (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 sign are reserved for header comment (10:1-10:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:92)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (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 sign are reserved for header comment (10:1-10:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:60)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (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 sign are reserved for header comment (10:1-10:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:97)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:53)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:92)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (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 sign are reserved for header comment (10:1-10:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Utilities.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Utilities.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Utilities.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Utilities.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Utilities.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Utilities.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Utilities.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Utilities.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Utilities.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:74)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Utilities.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Utilities.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:92)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Utilities.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Utilities.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/Attach10xBarcodes.wdl" @@ -37385,6 +39115,11 @@ 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 sign are reserved for header comment (24:25-24:72)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/sample_fastq.14.wdl" @@ -38165,6 +39900,81 @@ 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 sign are reserved for header comment (10:1-10:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:82)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" @@ -38200,6 +40010,81 @@ 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 sign are reserved for header comment (10:1-10:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:92)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:verification/VerifyCramToUnmappedBams.wdl" @@ -38770,6 +40655,81 @@ 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 sign are reserved for header comment (10:1-10:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:82)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:verification/VerifyImputation.wdl" @@ -38935,6 +40895,81 @@ 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 sign are reserved for header comment (10:1-10:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:82)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyImputation.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" @@ -39150,6 +41185,81 @@ 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 sign are reserved for header comment (10:1-10:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:92)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:verification/VerifyMultiSampleSmartSeq2.wdl" @@ -40105,6 +42215,16 @@ 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 sign are reserved for header comment (20:3-20:147)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (62:3-62:14)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" @@ -40240,6 +42360,16 @@ 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 sign are reserved for header comment (28:3-28:147)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (70:3-70:14)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" @@ -40310,6 +42440,81 @@ 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 sign are reserved for header comment (10:1-10:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:84)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:3)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:86)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:verification/VerifyscATAC.wdl" @@ -47265,6 +49470,26 @@ 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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (72:5-72:33)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" @@ -47455,6 +49680,16 @@ 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 sign are reserved for header comment (28:9-28:88)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (44:9-44:88)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" @@ -47770,6 +50005,26 @@ 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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (73:5-73:33)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" @@ -48865,6 +51120,31 @@ 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] header comments 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] header comments 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] header comments 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] header comments 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] header comments without a double pound sign (5:1-5:78)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/diamond/diamond.wdl" @@ -49070,21 +51350,61 @@ 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)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +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::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::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::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 (196:19-196:34)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (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 (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 (216:14-216:32)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +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 (224:6-224:18)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +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" @@ -49095,11 +51415,61 @@ 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)" +[[concerns]] 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must be snake case (284:6-284:27)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +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 (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 (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 (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 (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 (329:6-329:26)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" @@ -49110,26 +51480,91 @@ 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)" +[[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 = 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+[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +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 (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 (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 (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::W006::Naming/Low] identifier must be snake case (95:14-95:32)" +[[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" document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" @@ -51435,16 +53870,31 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" 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 (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_coverage_json (162:5-162:40)" +[[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 (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_contig_stats_json (163:5-163:37)" +[[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 (128:5-128:33)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -51480,6 +53930,11 @@ 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 (76:5-76:27)" +[[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 (161:5-161:32)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -51490,6 +53945,11 @@ 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 (159:5-159:23)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -51500,6 +53960,11 @@ 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)" +[[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 (129:5-129:35)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -51515,6 +53980,11 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (10:5-10:20)" +[[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 (160:5-160:49)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -51525,6 +53995,11 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_db (92:5-92:17)" +[[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 (130:5-130:20)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -51535,16 +54010,31 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (93:5-93:19)" +[[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 (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_blast_top_m8 (161:5-161:45)" +[[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 (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_hitsummary2_tab (160:5-160:48)" +[[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 (123:5-123:46)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -51675,126 +54165,251 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_nt_json (80:5-80:33)" +[[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 (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 task: use_taxon_whitelist (198:5-198:32)" +[[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 (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_coverage_json (234:5-234:40)" +[[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 (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_contig_stats_json (235:5-235:37)" +[[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 (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: contig_in_contigs_fasta (236:5-236:33)" +[[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 (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: docker_image_id (225:5-225:27)" +[[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 (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: duplicate_clusters_csv (240:5-240:32)" +[[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 (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_0 (237:5-237:18)" +[[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 (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: fastqs_1 (238:5-238:19)" +[[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 (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: file_ext (241:5-241:30)" +[[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 (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: gsnap_m8_gsnap_deduped_m8 (230:5-230:35)" +[[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 (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: lineage_db (245:5-245:90)" +[[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 (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: nonhost_fasta_refined_taxid_annot_fasta (239:5-239:49)" +[[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 (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_db (242:5-242:76)" +[[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 (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_info_db (244:5-244:89)" +[[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 (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: nt_loc_db (243:5-243:87)" +[[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 (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_blast_top_m8 (233:5-233:45)" +[[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 (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_hitsummary2_tab (232:5-232:48)" +[[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 (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: refined_gsnap_in_gsnap_reassigned_m8 (231:5-231:46)" +[[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 (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_bed (247:5-247:83)" +[[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 (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: resist_genome_db (246:5-246:80)" +[[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 (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: s3_wd_uri (226:5-226:21)" +[[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 (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_annotated_merged_fa (227:5-227:44)" +[[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 (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_gsnap_hitsummary_tab (228:5-228:45)" +[[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 (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: taxid_fasta_in_rapsearch2_hitsummary_tab (229:5-229:50)" +[[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 (212:5-212:40)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -51805,11 +54420,36 @@ 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)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (119:6-119:25)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" 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 (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 (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 (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 (129:10-129:35)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -51825,6 +54465,11 @@ 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 (155:6-155:18)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -51855,16 +54500,56 @@ 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 (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 (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 (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 (191:6-191:18)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +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 (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 (194:12-194:21)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +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 (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 (197:10-197:45)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -51905,6 +54590,16 @@ 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)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +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 (300:11-300:45)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -52830,6 +55525,31 @@ 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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (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 sign are reserved for header comment (714:1-714:100)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" @@ -54785,6 +57505,91 @@ 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" @@ -54810,6 +57615,16 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/cellranger.wdl" 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 (139:11-139:21)" + +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (140:11-140:21)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/fq.wdl" @@ -54820,6 +57635,16 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/fq.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (142:11-142:21)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/fq.wdl" +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 (150:12-150:18)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/fq.wdl" @@ -54830,6 +57655,16 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/fq.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (152:12-152:18)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/fq.wdl" +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 (167:15-167:31)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/fq.wdl" @@ -54840,6 +57675,16 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/fq.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (169:15-169:31)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/fq.wdl" +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 (72:11-72:21)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/fq.wdl" @@ -54850,6 +57695,46 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/fq.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (74:11-74:21)" +[[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 (347:11-347:21)" + +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/kraken2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (348:11-348:21)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/kraken2.wdl" @@ -54865,6 +57750,11 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/librarian.wdl" 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 (36:14-36:20)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/md5sum.wdl" @@ -54875,21 +57765,66 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/picard.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (119:15-119:39)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/picard.wdl" +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)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/picard.wdl" +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)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/picard.wdl" +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)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/picard.wdl" +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] header comments without a double pound sign (2:1-2:2)" + +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/sambamba.wdl" +message = "[v1::W010::Style/Low] header comments without a double pound sign (3:1-3:31)" + +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/sambamba.wdl" +message = "[v1::W010::Style/Low] header comments 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 (478:20-478:47)" + +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (479:19-479:41)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -54900,36 +57835,81 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (481:19-481:41)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (487:19-487:44)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (493:19-493:43)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (499:19-499:46)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (505:19-505:44)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (510:28-510:44)" + +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (511:30-511:46)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (512:28-512:44)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (513:24-513:48)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -54940,11 +57920,21 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" 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 (515:16-515:33)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (515:24-515:48)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (516:16-516:31)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -54960,21 +57950,46 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (518:16-518:31)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (519:16-519:30)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (519:16-519:33)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (520:16-520:32)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (521:16-521:30)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (522:16-522:26)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -54985,21 +58000,46 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (523:16-523:28)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (524:16-524:26)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (525:16-525:29)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (526:16-526:32)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (526:16-526:37)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (527:16-527:29)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55010,16 +58050,36 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (528:16-528:32)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (529:16-529:29)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (530:16-530:27)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (530:16-530:44)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (531:16-531:26)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55030,26 +58090,51 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (532:16-532:27)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (533:16-533:26)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (534:16-534:37)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (535:16-535:27)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (537:15-537:41)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (538:15-538:42)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55060,26 +58145,61 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (539:15-539:41)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (53:16-53:32)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (540:15-540:42)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (541:15-541:42)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (542:15-542:27)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (542:15-542:43)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (543:15-543:47)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (544:13-544:22)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55090,16 +58210,36 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (545:13-545:23)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (546:13-546:22)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (547:13-547:26)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (548:13-548:32)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55110,26 +58250,61 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (549:13-549:30)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (54:16-54:34)" + +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (550:13-550:32)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (551:13-551:31)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (552:13-552:31)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (553:13-553:30)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (554:13-554:26)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55140,21 +58315,46 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (555:13-555:25)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (556:13-556:26)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (557:13-557:34)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (557:13-557:40)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (558:13-558:34)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (559:13-559:31)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55165,11 +58365,26 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (55:16-55:32)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (560:13-560:21)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (560:13-560:30)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (561:13-561:27)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55180,6 +58395,16 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (562:13-562:21)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (563:13-563:25)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55210,21 +58435,46 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (568:13-568:25)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (569:13-569:25)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (56:16-56:34)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (570:13-570:27)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (570:13-570:31)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (571:13-571:29)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55235,21 +58485,46 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (572:13-572:27)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (573:13-573:29)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (574:13-574:28)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (575:13-575:25)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (575:13-575:30)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (576:13-576:23)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55260,16 +58535,36 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (577:13-577:25)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (578:13-578:23)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (579:13-579:27)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (57:16-57:44)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55280,46 +58575,96 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (580:13-580:27)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (581:13-581:29)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (582:13-582:31)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (583:13-583:33)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (584:13-584:36)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (585:13-585:36)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (586:13-586:31)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (586:13-586:42)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (587:13-587:40)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (588:13-588:31)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (589:13-589:31)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55330,16 +58675,36 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (58:16-58:40)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (590:13-590:24)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (591:13-591:27)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (591:13-591:31)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (592:13-592:25)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55350,21 +58715,46 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (593:13-593:27)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (594:13-594:25)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (595:13-595:29)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (596:13-596:32)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (597:13-597:34)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55375,6 +58765,11 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" 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 (599:13-599:29)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55385,6 +58780,11 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (59:16-59:44)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (600:13-600:35)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55395,6 +58795,16 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (601:13-601:29)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (602:13-602:27)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55410,11 +58820,26 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (604:13-604:27)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (60:16-60:44)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (62:13-62:28)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55425,6 +58850,16 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (63:13-63:32)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (64:13-64:25)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55440,6 +58875,16 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (66:13-66:25)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +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 (817:9-817:30)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55455,16 +58900,36 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (820:9-820:30)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/util.wdl" +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 (26:17-26:23)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/util.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (413:14-413:21)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/util.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (415:14-415:21)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:workflows/general/bam-to-fastqs.wdl" +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 (50:22-50:28)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/general/bam-to-fastqs.wdl" @@ -55475,11 +58940,21 @@ 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)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:workflows/qc/quality-check-standard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (570:11-570:35)" + [[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)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:workflows/reference/bwa-db-build.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:17-26:33)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/reference/bwa-db-build.wdl" @@ -55487,93 +58962,123 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (28:17-28:33)" [[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] header comments 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] header comments 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/make-qc-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (127:14-127:21)" [[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 (33:17-33:33)" + +[[concerns]] +kind = "LintWarning" +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/reference/star-db-build.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:17-35:33)" + +[[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)" [[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] header comments 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] header comments without a double pound sign (2:1-2:50)" [[concerns]] kind = "LintWarning" diff --git a/RULES.md b/RULES.md index b27959bd..ef167c73 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] | +| `header_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..ea2fdbfa 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 `header_comment` rule for header comment 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..579c39dc 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) | +//! | `header_comment` | `v1::W010` | Style | [Link](lint::HeaderComment) | 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..741e973c 100644 --- a/wdl-grammar/src/v1/lint.rs +++ b/wdl-grammar/src/v1/lint.rs @@ -2,6 +2,7 @@ use pest::iterators::Pair; +mod header_comment; mod missing_runtime_block; mod mixed_indentation; mod newline_eof; @@ -9,6 +10,7 @@ mod no_curly_commands; mod snake_case; mod whitespace; +pub use header_comment::HeaderComment; pub use missing_runtime_block::MissingRuntimeBlock; pub use mixed_indentation::MixedIndentation; pub use newline_eof::NewlineEOF; @@ -31,5 +33,7 @@ pub fn rules<'a>() -> Vec HeaderComment { + /// Creates a warning for header 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("header comments without a double pound sign") + .body( + "Header 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 header comments after version declaration + fn header_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 sign are reserved for header comment") + .body( + "Only full line comment before 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 HeaderComment { + 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_header = true; + + for node in tree.clone().into_inner().flatten() { + match node.as_rule() { + v1::Rule::version => { + is_header = false; + } + v1::Rule::COMMENT => { + // Catches missing double pound sign + if is_header & !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 header comment after version declaration + if !is_header & node.as_str().starts_with("##") { + let location = + Location::try_from(node.as_span()).map_err(lint::Error::Location)?; + warnings.push_back(self.header_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_header_comment() -> Result<(), Box> { + let tree = Parser::parse( + Rule::document, + r#"# a comment +version 1.0 +"#, + )? + .next() + .unwrap(); + + let warnings = HeaderComment.check(&tree)?.unwrap(); + assert_eq!(warnings.len(), 1); + assert_eq!( + warnings.first().to_string(), + "[v1::W010::Style/Low] header comments without a double pound sign (1:1-1:12)" + ); + Ok(()) + } + + #[test] + fn it_catches_header_comment_after_version() -> Result<(), Box> { + let tree = Parser::parse( + Rule::document, + r#"## a comment +version 1.0 + +## a wrong comment +"#, + )? + .next() + .unwrap(); + + let warnings = HeaderComment.check(&tree)?.unwrap(); + assert_eq!(warnings.len(), 1); + assert_eq!( + warnings.first().to_string(), + "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:19)" + ); + Ok(()) + } + + #[test] + fn it_ignores_a_properly_formatted_header_comment() -> Result<(), Box> { + let tree = Parser::parse( + Rule::document, + r#"## a comment +version 1.0 +"#, + )? + .next() + .unwrap(); + let warnings = HeaderComment.check(&tree)?; + assert!(warnings.is_none()); + Ok(()) + } +} From 372b1199c88c0710217f564139e2b24b594c85e6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Wed, 8 May 2024 22:19:29 -0400 Subject: [PATCH 2/6] feat: update Gauntlet toml --- Gauntlet.toml | 1520 +++++++------------------------------------------ 1 file changed, 205 insertions(+), 1315 deletions(-) diff --git a/Gauntlet.toml b/Gauntlet.toml index d334a06c..21478b3a 100644 --- a/Gauntlet.toml +++ b/Gauntlet.toml @@ -51290,66 +51290,6 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/host-genome-generation/run.wdl" 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)" - -[[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)" - -[[concerns]] -kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" -message = "[v1::W001::Style/Low] trailing space (418:15)" - -[[concerns]] -kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" -message = "[v1::W001::Style/Low] trailing space (88:10)" - -[[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)" - -[[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)" - -[[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)" - -[[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)" - -[[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)" - -[[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)" - -[[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)" - -[[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)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" @@ -51370,11 +51310,6 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" 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 (196:19-196:34)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" @@ -51385,36 +51320,16 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" 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 (216:14-216:32)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" 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 (224:6-224:18)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" 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 (244:6-244:18)" - -[[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)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" @@ -51435,11 +51350,6 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" 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 (284:6-284:27)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" @@ -51470,46 +51380,21 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" 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 (346:6-346:23)" - -[[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)" - [[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 (429:6-429:27)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" 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 (434:16-434:17)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" 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 (459:19-459:33)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" @@ -51555,11 +51440,6 @@ 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::W006::Naming/Low] identifier must be snake case (95:14-95:32)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" @@ -53875,31 +53755,16 @@ 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 (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_coverage_json (162:5-162:40)" - [[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 (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_contig_stats_json (163:5-163:37)" - [[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 (128:5-128:33)" -[[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)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -53910,11 +53775,6 @@ 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" @@ -53935,41 +53795,16 @@ 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 (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: 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 (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: fastqs (195:5-195:23)" - -[[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)" - [[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 (129:5-129:35)" -[[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)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -53985,11 +53820,6 @@ 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 (160:5-160:49)" -[[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)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -54000,11 +53830,6 @@ 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 (130:5-130:20)" -[[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)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -54015,41 +53840,16 @@ 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 (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_blast_top_m8 (161:5-161:45)" - [[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 (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_hitsummary2_tab (160:5-160:48)" - [[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 (123:5-123:46)" -[[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)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -54060,11 +53860,6 @@ 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" @@ -54170,11 +53965,6 @@ 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 (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 task: use_taxon_whitelist (198:5-198:32)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" @@ -54183,522 +53973,262 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within workflo [[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_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_contig_stats_json (199:5-199:37)" +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: contig_in_contig_stats_json (235:5-235:37)" +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: contig_in_contigs_fasta (200:5-200:33)" +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: contig_in_contigs_fasta (236:5-236:33)" +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: docker_image_id (189:5-189:27)" +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: docker_image_id (225:5-225:27)" +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: duplicate_clusters_csv (204:5-204:32)" +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: duplicate_clusters_csv (240:5-240:32)" +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: fastqs_0 (201:5-201:18)" +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: fastqs_0 (237:5-237:18)" +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: fastqs_1 (202:5-202:19)" +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: fastqs_1 (238:5-238:19)" +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: file_ext (205:5-205:30)" +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: file_ext (241:5-241:30)" +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: gsnap_m8_gsnap_deduped_m8 (194:5-194:35)" +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: gsnap_m8_gsnap_deduped_m8 (230:5-230:35)" +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: lineage_db (209:5-209:90)" +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: lineage_db (245:5-245:90)" +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: nonhost_fasta_refined_taxid_annot_fasta (203:5-203:49)" +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: nonhost_fasta_refined_taxid_annot_fasta (239:5-239:49)" +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: nt_db (206:5-206:76)" +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: nt_db (242:5-242:76)" +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::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (208:5-208:89)" +message = "[v1::W006::Naming/Low] identifier must be snake case (119:6-119:25)" [[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::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::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (207:5-207:87)" +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::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (243:5-243:87)" +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::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_blast_top_m8 (197:5-197:45)" +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::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_blast_top_m8 (233:5-233:45)" +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::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_hitsummary2_tab (196:5-196:48)" +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::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_hitsummary2_tab (232:5-232:48)" +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::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_reassigned_m8 (195:5-195:46)" +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::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_reassigned_m8 (231:5-231:46)" +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::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_bed (211:5-211:83)" +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::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_bed (247:5-247:83)" +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::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_db (210:5-210:80)" +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::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_db (246:5-246:80)" +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::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (190:5-190:21)" +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::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (226:5-226:21)" +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::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_annotated_merged_fa (191:5-191:44)" +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::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_annotated_merged_fa (227:5-227:44)" +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::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_gsnap_hitsummary_tab (192:5-192:45)" +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::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_gsnap_hitsummary_tab (228:5-228:45)" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:12-37:21)" [[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_rapsearch2_hitsummary_tab (193:5-193:50)" +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/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_rapsearch2_hitsummary_tab (229:5-229:50)" +message = "[v1::W006::Naming/Low] identifier must be snake case (6:12-6:21)" [[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 (212:5-212:40)" +message = "[v1::W006::Naming/Low] identifier must be snake case (74:6-74:26)" [[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::W006::Naming/Low] identifier must be snake case (77:12-77:21)" [[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 (78:10-78:35)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (119:6-119:25)" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (122:12-122:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: adapter_fasta (351:5-351:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (123:10-123:46)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (868:5-868:13)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -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 (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 (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 (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 (155:6-155:18)" - -[[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 (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 (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 (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 (191:6-191:18)" - -[[concerns]] -kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -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 (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 (194:12-194:21)" - -[[concerns]] -kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -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 (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 (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 (214:10-214:26)" - -[[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)" - -[[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)" - -[[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)" - -[[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)" - -[[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)" - -[[concerns]] -kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake 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"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 (598:13-598:36)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (61:13-61:32)" +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 (62:13-62:28)" +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 (62:13-62:30)" +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 (63:13-63:32)" +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 (63:13-63:34)" +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 (64:13-64:25)" +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" @@ -58890,36 +57835,16 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (818:9-818:30)" -[[concerns]] -kind = "LintWarning" -document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (819:9-819:30)" - -[[concerns]] -kind = "LintWarning" -document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (820:9-820:30)" - [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/util.wdl" 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 (26:17-26:23)" - [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/util.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (413:14-413:21)" -[[concerns]] -kind = "LintWarning" -document = "stjudecloud/workflows:tools/util.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (415:14-415:21)" - [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/general/bam-to-fastqs.wdl" @@ -58930,36 +57855,16 @@ kind = "LintWarning" document = "stjudecloud/workflows:workflows/general/bam-to-fastqs.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (50:22-50:28)" -[[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)" - -[[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)" - [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/qc/quality-check-standard.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (570:11-570:35)" -[[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)" - [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/reference/bwa-db-build.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (26:17-26:33)" -[[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)" - [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" @@ -59030,11 +57935,6 @@ kind = "LintWarning" 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/reference/make-qc-reference.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (127:14-127:21)" - [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/reference/star-db-build.wdl" @@ -59045,16 +57945,6 @@ kind = "LintWarning" 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/reference/star-db-build.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (35:17-35:33)" - -[[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)" - [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-variant-calling.wdl" From 248512a668234589d63c5092c5b9462765400994 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Sat, 11 May 2024 19:19:46 -0400 Subject: [PATCH 3/6] feat: updating naming convention --- Gauntlet.toml | 1612 +++++++++-------- RULES.md | 2 +- lint-rules.md | 10 +- wdl-grammar/CHANGELOG.md | 4 +- wdl-grammar/src/v1.rs | 2 +- wdl-grammar/src/v1/lint.rs | 6 +- ...{header_comment.rs => preamble_comment.rs} | 54 +- 7 files changed, 881 insertions(+), 809 deletions(-) rename wdl-grammar/src/v1/lint/{header_comment.rs => preamble_comment.rs} (67%) diff --git a/Gauntlet.toml b/Gauntlet.toml index 21478b3a..54c0f182 100644 --- a/Gauntlet.toml +++ b/Gauntlet.toml @@ -3063,97 +3063,97 @@ message = "[v1::W007::Spacing/Low] missing newline at the end of the file (66:2- [[concerns]] kind = "LintWarning" document = "biowdl/tasks:deconstructsigs.wdl" -message = "[v1::W010::Style/Low] header comments without a double pound sign (10:1-10:77)" +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] header comments without a double pound sign (11:1-11:54)" +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] header comments without a double pound sign (12:1-12:2)" +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] header comments without a double pound sign (13:1-13:77)" +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] header comments without a double pound sign (14:1-14:75)" +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] header comments without a double pound sign (15:1-15:78)" +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] header comments without a double pound sign (16:1-16:73)" +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] header comments without a double pound sign (17:1-17:80)" +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] header comments without a double pound sign (18:1-18:80)" +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] header comments without a double pound sign (19:1-19:12)" +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] header comments without a double pound sign (1:1-1:54)" +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] header comments without a double pound sign (2:1-2:2)" +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] header comments without a double pound sign (3:1-3:79)" +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] header comments without a double pound sign (4:1-4:80)" +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] header comments without a double pound sign (5:1-5:79)" +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] header comments without a double pound sign (6:1-6:76)" +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] header comments without a double pound sign (7:1-7:72)" +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] header comments without a double pound sign (8:1-8:59)" +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] header comments without a double pound sign (9:1-9:2)" +message = "[v1::W010::Style/Low] preamble comment without a double pound sign (9:1-9:2)" [[concerns]] kind = "LintWarning" @@ -17243,47 +17243,47 @@ 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 sign are reserved for header comment (10:1-10:86)" +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 sign are reserved for header comment (11:1-11:62)" +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 sign are reserved for header comment (3:1-3:35)" +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 sign are reserved for header comment (4:1-4:3)" +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 sign are reserved for header comment (5:1-5:15)" +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 sign are reserved for header comment (6:1-6:85)" +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 sign are reserved for header comment (7:1-7:87)" +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 sign are reserved for header comment (8:1-8:86)" +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 sign are reserved for header comment (9:1-9:84)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:84)" [[concerns]] kind = "LintWarning" @@ -17723,77 +17723,77 @@ 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 sign are reserved for header comment (10:1-10:3)" +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 sign are reserved for header comment (11:1-11:15)" +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 sign are reserved for header comment (12:1-12:85)" +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 sign are reserved for header comment (13:1-13:87)" +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 sign are reserved for header comment (14:1-14:86)" +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 sign are reserved for header comment (15:1-15:84)" +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 sign are reserved for header comment (16:1-16:86)" +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 sign are reserved for header comment (17:1-17:62)" +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 sign are reserved for header comment (3:1-3:35)" +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 sign are reserved for header comment (4:1-4:3)" +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 sign are reserved for header comment (5:1-5:92)" +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 sign are reserved for header comment (6:1-6:3)" +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 sign are reserved for header comment (7:1-7:3)" +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 sign are reserved for header comment (8:1-8:86)" +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 sign are reserved for header comment (9:1-9:48)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:48)" [[concerns]] kind = "LintWarning" @@ -18098,77 +18098,77 @@ 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 sign are reserved for header comment (10:1-10:79)" +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 sign are reserved for header comment (11:1-11:3)" +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 sign are reserved for header comment (12:1-12:3)" +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 sign are reserved for header comment (13:1-13:86)" +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 sign are reserved for header comment (14:1-14:48)" +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 sign are reserved for header comment (15:1-15:3)" +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 sign are reserved for header comment (16:1-16:15)" +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 sign are reserved for header comment (17:1-17:85)" +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 sign are reserved for header comment (18:1-18:87)" +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 sign are reserved for header comment (19:1-19:86)" +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 sign are reserved for header comment (20:1-20:84)" +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 sign are reserved for header comment (21:1-21:86)" +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 sign are reserved for header comment (22:1-22:62)" +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 sign are reserved for header comment (8:1-8:35)" +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 sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -18393,77 +18393,77 @@ 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 sign are reserved for header comment (10:1-10:3)" +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 sign are reserved for header comment (11:1-11:86)" +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 sign are reserved for header comment (12:1-12:48)" +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 sign are reserved for header comment (13:1-13:3)" +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 sign are reserved for header comment (14:1-14:15)" +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 sign are reserved for header comment (15:1-15:85)" +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 sign are reserved for header comment (16:1-16:87)" +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 sign are reserved for header comment (17:1-17:86)" +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 sign are reserved for header comment (18:1-18:84)" +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 sign are reserved for header comment (19:1-19:86)" +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 sign are reserved for header comment (20:1-20:62)" +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 sign are reserved for header comment (6:1-6:35)" +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 sign are reserved for header comment (7:1-7:3)" +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 sign are reserved for header comment (8:1-8:80)" +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 sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -19413,162 +19413,162 @@ 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 sign are reserved for header comment (10:1-10:70)" +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 sign are reserved for header comment (11:1-11:102)" +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 sign are reserved for header comment (12:1-12:21)" +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 sign are reserved for header comment (13:1-13:3)" +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 sign are reserved for header comment (14:1-14:31)" +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 sign are reserved for header comment (15:1-15:63)" +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 sign are reserved for header comment (16:1-16:87)" +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 sign are reserved for header comment (17:1-17:80)" +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 sign are reserved for header comment (18:1-18:67)" +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 sign are reserved for header comment (19:1-19:53)" +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 sign are reserved for header comment (20:1-20:48)" +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 sign are reserved for header comment (21:1-21:37)" +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" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (22:1-22:47)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (22:1-22:47)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (23:1-23:52)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (23:1-23:52)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (24:1-24:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (24:1-24:3)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (25:1-25:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (25:1-25:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (26:1-26:48)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (26:1-26:48)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (27:1-27:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (27:1-27:3)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (28:1-28:15)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (28:1-28:15)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (29:1-29:85)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (29:1-29:85)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (30:1-30:87)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (30:1-30:87)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (31:1-31:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (31:1-31:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (32:1-32:84)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (32:1-32:84)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (33:1-33:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (33:1-33:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (34:1-34:62)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (34:1-34:62)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" +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/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" +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/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:85)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:85)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:51)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:51)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:3)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:112)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:112)" [[concerns]] kind = "LintWarning" @@ -19728,137 +19728,137 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (94:11-94:37)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:79)" +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/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:87)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:87)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:80)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:80)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:67)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:67)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:53)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:53)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:48)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:48)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:37)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:37)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:47)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:47)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:52)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:52)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (19:1-19:3)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (20:1-20:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (21:1-21:48)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (21:1-21:48)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (22:1-22:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (22:1-22:3)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (23:1-23:15)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (23:1-23:15)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (24:1-24:85)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (24:1-24:85)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (25:1-25:87)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (25:1-25:87)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (26:1-26:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (26:1-26:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (27:1-27:84)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (27:1-27:84)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (28:1-28:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (28:1-28:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (29:1-29:62)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (29:1-29:62)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" +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/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" +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/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:85)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (6:1-6:85)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:47)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (7:1-7:47)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:3)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:31)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:31)" [[concerns]] kind = "LintWarning" @@ -21053,77 +21053,77 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (40:10-40:25)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:3)" +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/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:86)" +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/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:48)" +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/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:3)" +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/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:15)" +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/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:85)" +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/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:87)" +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/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:86)" +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/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:84)" +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/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:86)" +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/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:62)" +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/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:35)" +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/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:3)" +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/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:79)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:79)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -21978,82 +21978,82 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (25:10-25:26)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:56)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:56)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:140)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:140)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:153)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:153)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:291-13:293)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:291-13:293)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:86)" +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/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:48)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:48)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:3)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:15)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:15)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:85)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:85)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:87)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (19:1-19:87)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (20:1-20:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (21:1-21:84)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (21:1-21:84)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (22:1-22:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (22:1-22:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (23:1-23:62)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (23:1-23:62)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:35)" +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/qc/CheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -22828,72 +22828,72 @@ message = "[v1::W007::Spacing/Low] multiple empty lines at the end of file (259: [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:48)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:48)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:3)" +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/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:15)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:15)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:85)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:85)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:87)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:87)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:86)" +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/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:84)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:84)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:62)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (19:1-19:62)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:35)" +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/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:3)" +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/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:66)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (8:1-8:66)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -23733,7 +23733,7 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (972:6-972:18)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (333:5-333:13)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (333:5-333:13)" [[concerns]] kind = "LintWarning" @@ -24943,62 +24943,62 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (31:22-31:30)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:35)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (10:1-10:35)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (11:1-11:3)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:66)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (12:1-12:66)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (13:1-13:3)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (14:1-14:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:48)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (15:1-15:48)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (16:1-16:3)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (17:1-17:15)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (17:1-17:15)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (18:1-18:85)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (18:1-18:85)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (19:1-19:87)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (19:1-19:87)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (20:1-20:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (20:1-20:86)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (21:1-21:63)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (21:1-21:63)" [[concerns]] kind = "LintWarning" @@ -25128,17 +25128,17 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (6:10-6:30)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (134:3-134:44)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (134:3-134:44)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (149:3-149:26)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (149:3-149:26)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (80:3-80:32)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (80:3-80:32)" [[concerns]] kind = "LintWarning" @@ -25203,12 +25203,12 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (31:21-31:39)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (129:3-129:44)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (129:3-129:44)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (145:3-145:26)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (145:3-145:26)" [[concerns]] kind = "LintWarning" @@ -26833,17 +26833,17 @@ message = "[v1::W007::Spacing/Low] multiple empty lines at the end of file (235: [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (109:3-109:83)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (109:3-109:83)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (190:3-190:85)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (190:3-190:85)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (43:3-43:70)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (43:3-43:70)" [[concerns]] kind = "LintWarning" @@ -27043,17 +27043,17 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (8:10-8:34)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (120:3-120:79)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (120:3-120:79)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (204:3-204:85)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (204:3-204:85)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (40:3-40:70)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (40:3-40:70)" [[concerns]] kind = "LintWarning" @@ -28403,7 +28403,7 @@ message = "[v1::W007::Spacing/Low] missing newline at the end of the file (287:2 [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (40:31-40:59)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (40:31-40:59)" [[concerns]] kind = "LintWarning" @@ -28698,77 +28698,77 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (90:10-90:43)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:15)" +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/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:85)" +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/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:87)" +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/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:86)" +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/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:84)" +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/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:86)" +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/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:62)" +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/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (2:1-2:35)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (2:1-2:35)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (3:1-3:3)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:97)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (4:1-4:97)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:53)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:53)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:3)" +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/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:92)" +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/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:48)" +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/AggregatedBamQC.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -28853,72 +28853,72 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (21:6-21:31)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:15)" +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/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:85)" +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/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:87)" +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/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:86)" +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/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:84)" +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/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:86)" +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/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:62)" +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/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" +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/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" +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/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:93)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:93)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:3)" +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/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:92)" +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/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:48)" +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/Alignment.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -29408,72 +29408,72 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (64:6-64:20)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:15)" +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/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:85)" +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/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:87)" +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/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (13:1-13:86)" +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/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (14:1-14:84)" +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/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (15:1-15:86)" +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/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (16:1-16:62)" +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/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (3:1-3:35)" +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/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:3)" +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/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (5:1-5:103)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (5:1-5:103)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (6:1-6:3)" +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/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (7:1-7:92)" +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/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (8:1-8:48)" +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/BamProcessing.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -29658,72 +29658,72 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (18:6-18:31)" [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:15)" +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/CopyFilesFromCloudToCloud.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (11:1-11:85)" +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/CopyFilesFromCloudToCloud.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (12:1-12:87)" +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 sign are reserved for header comment (13:1-13:86)" +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 sign are reserved for header comment (14:1-14:84)" +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 sign are reserved for header comment (15:1-15:86)" +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 sign are reserved for header comment (16:1-16:62)" +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 sign are reserved for header comment (3:1-3:35)" +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 sign are reserved for header comment (4:1-4:3)" +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 sign are reserved for header comment (5:1-5:94)" +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 sign are reserved for header comment (6:1-6:3)" +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 sign are reserved for header comment (7:1-7:92)" +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 sign are reserved for header comment (8:1-8:48)" +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 sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -29813,82 +29813,82 @@ 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 sign are reserved for header comment (10:1-10:3)" +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 sign are reserved for header comment (11:1-11:15)" +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 sign are reserved for header comment (12:1-12:85)" +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 sign are reserved for header comment (13:1-13:87)" +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 sign are reserved for header comment (14:1-14:86)" +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 sign are reserved for header comment (15:1-15:84)" +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 sign are reserved for header comment (16:1-16:86)" +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 sign are reserved for header comment (17:1-17:62)" +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 sign are reserved for header comment (25:20-25:46)" +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 sign are reserved for header comment (3:1-3:35)" +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 sign are reserved for header comment (4:1-4:3)" +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 sign are reserved for header comment (5:1-5:88)" +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 sign are reserved for header comment (6:1-6:55)" +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 sign are reserved for header comment (7:1-7:3)" +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 sign are reserved for header comment (8:1-8:92)" +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 sign are reserved for header comment (9:1-9:48)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:48)" [[concerns]] kind = "LintWarning" @@ -29958,72 +29958,72 @@ 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 sign are reserved for header comment (10:1-10:15)" +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 sign are reserved for header comment (11:1-11:85)" +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 sign are reserved for header comment (12:1-12:87)" +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 sign are reserved for header comment (13:1-13:86)" +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 sign are reserved for header comment (14:1-14:84)" +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 sign are reserved for header comment (15:1-15:86)" +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 sign are reserved for header comment (16:1-16:62)" +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 sign are reserved for header comment (3:1-3:35)" +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 sign are reserved for header comment (4:1-4:3)" +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 sign are reserved for header comment (5:1-5:136)" +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 sign are reserved for header comment (6:1-6:3)" +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 sign are reserved for header comment (7:1-7:92)" +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 sign are reserved for header comment (8:1-8:48)" +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 sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -34603,72 +34603,72 @@ 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 sign are reserved for header comment (10:1-10:15)" +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 sign are reserved for header comment (11:1-11:85)" +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 sign are reserved for header comment (12:1-12:87)" +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 sign are reserved for header comment (13:1-13:86)" +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 sign are reserved for header comment (14:1-14:84)" +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 sign are reserved for header comment (15:1-15:86)" +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 sign are reserved for header comment (16:1-16:62)" +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 sign are reserved for header comment (3:1-3:35)" +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 sign are reserved for header comment (4:1-4:3)" +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 sign are reserved for header comment (5:1-5:86)" +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 sign are reserved for header comment (6:1-6:3)" +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 sign are reserved for header comment (7:1-7:92)" +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 sign are reserved for header comment (8:1-8:48)" +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 sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -35928,72 +35928,72 @@ 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 sign are reserved for header comment (10:1-10:48)" +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 sign are reserved for header comment (11:1-11:3)" +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 sign are reserved for header comment (12:1-12:15)" +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 sign are reserved for header comment (13:1-13:85)" +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 sign are reserved for header comment (14:1-14:87)" +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 sign are reserved for header comment (15:1-15:86)" +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 sign are reserved for header comment (16:1-16:84)" +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 sign are reserved for header comment (17:1-17:86)" +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 sign are reserved for header comment (18:1-18:62)" +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 sign are reserved for header comment (5:1-5:35)" +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 sign are reserved for header comment (6:1-6:3)" +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 sign are reserved for header comment (7:1-7:60)" +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 sign are reserved for header comment (8:1-8:3)" +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 sign are reserved for header comment (9:1-9:86)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:86)" [[concerns]] kind = "LintWarning" @@ -36578,77 +36578,77 @@ 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 sign are reserved for header comment (10:1-10:3)" +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 sign are reserved for header comment (11:1-11:15)" +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 sign are reserved for header comment (12:1-12:85)" +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 sign are reserved for header comment (13:1-13:87)" +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 sign are reserved for header comment (14:1-14:86)" +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 sign are reserved for header comment (15:1-15:84)" +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 sign are reserved for header comment (16:1-16:86)" +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 sign are reserved for header comment (17:1-17:62)" +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 sign are reserved for header comment (3:1-3:35)" +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 sign are reserved for header comment (4:1-4:3)" +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 sign are reserved for header comment (5:1-5:97)" +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 sign are reserved for header comment (6:1-6:53)" +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 sign are reserved for header comment (7:1-7:3)" +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 sign are reserved for header comment (8:1-8:92)" +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 sign are reserved for header comment (9:1-9:48)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:48)" [[concerns]] kind = "LintWarning" @@ -36828,72 +36828,72 @@ message = "[v1::W007::Spacing/Low] missing newline at the end of the file (301:2 [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:15)" +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 sign are reserved for header comment (11:1-11:85)" +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 sign are reserved for header comment (12:1-12:87)" +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 sign are reserved for header comment (13:1-13:86)" +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 sign are reserved for header comment (14:1-14:84)" +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 sign are reserved for header comment (15:1-15:86)" +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 sign are reserved for header comment (16:1-16:62)" +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 sign are reserved for header comment (3:1-3:35)" +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 sign are reserved for header comment (4:1-4:3)" +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 sign are reserved for header comment (5:1-5:74)" +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 sign are reserved for header comment (6:1-6:3)" +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 sign are reserved for header comment (7:1-7:92)" +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 sign are reserved for header comment (8:1-8:48)" +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 sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -38223,112 +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" @@ -39118,7 +39133,7 @@ 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 sign are reserved for header comment (24:25-24:72)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (24:25-24:72)" [[concerns]] kind = "LintWarning" @@ -39903,77 +39918,77 @@ message = "[v1::W007::Spacing/Low] multiple empty lines at the end of file (78:1 [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:3)" +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 sign are reserved for header comment (11:1-11:86)" +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 sign are reserved for header comment (12:1-12:48)" +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 sign are reserved for header comment (13:1-13:3)" +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 sign are reserved for header comment (14:1-14:15)" +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 sign are reserved for header comment (15:1-15:85)" +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 sign are reserved for header comment (16:1-16:87)" +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 sign are reserved for header comment (17:1-17:86)" +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 sign are reserved for header comment (18:1-18:84)" +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 sign are reserved for header comment (19:1-19:86)" +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 sign are reserved for header comment (20:1-20:62)" +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 sign are reserved for header comment (6:1-6:35)" +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 sign are reserved for header comment (7:1-7:3)" +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 sign are reserved for header comment (8:1-8:82)" +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 sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -40013,77 +40028,77 @@ message = "[v1::W007::Spacing/Low] multiple empty lines at the end of file (55:1 [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:3)" +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 sign are reserved for header comment (11:1-11:86)" +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 sign are reserved for header comment (12:1-12:48)" +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 sign are reserved for header comment (13:1-13:3)" +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 sign are reserved for header comment (14:1-14:15)" +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 sign are reserved for header comment (15:1-15:85)" +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 sign are reserved for header comment (16:1-16:87)" +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 sign are reserved for header comment (17:1-17:86)" +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 sign are reserved for header comment (18:1-18:84)" +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 sign are reserved for header comment (19:1-19:86)" +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 sign are reserved for header comment (20:1-20:62)" +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 sign are reserved for header comment (6:1-6:35)" +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 sign are reserved for header comment (7:1-7:3)" +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 sign are reserved for header comment (8:1-8:92)" +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 sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -40658,77 +40673,77 @@ 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 sign are reserved for header comment (10:1-10:3)" +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 sign are reserved for header comment (11:1-11:86)" +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 sign are reserved for header comment (12:1-12:48)" +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 sign are reserved for header comment (13:1-13:3)" +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 sign are reserved for header comment (14:1-14:15)" +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 sign are reserved for header comment (15:1-15:85)" +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 sign are reserved for header comment (16:1-16:87)" +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 sign are reserved for header comment (17:1-17:86)" +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 sign are reserved for header comment (18:1-18:84)" +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 sign are reserved for header comment (19:1-19:86)" +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 sign are reserved for header comment (20:1-20:62)" +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 sign are reserved for header comment (6:1-6:35)" +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 sign are reserved for header comment (7:1-7:3)" +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 sign are reserved for header comment (8:1-8:82)" +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 sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -40898,77 +40913,77 @@ message = "[v1::W007::Spacing/Low] missing newline at the end of the file (177:2 [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:3)" +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 sign are reserved for header comment (11:1-11:86)" +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 sign are reserved for header comment (12:1-12:48)" +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 sign are reserved for header comment (13:1-13:3)" +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 sign are reserved for header comment (14:1-14:15)" +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 sign are reserved for header comment (15:1-15:85)" +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 sign are reserved for header comment (16:1-16:87)" +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 sign are reserved for header comment (17:1-17:86)" +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 sign are reserved for header comment (18:1-18:84)" +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 sign are reserved for header comment (19:1-19:86)" +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 sign are reserved for header comment (20:1-20:62)" +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 sign are reserved for header comment (6:1-6:35)" +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 sign are reserved for header comment (7:1-7:3)" +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 sign are reserved for header comment (8:1-8:82)" +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 sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -41188,77 +41203,77 @@ 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 sign are reserved for header comment (10:1-10:86)" +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 sign are reserved for header comment (11:1-11:48)" +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 sign are reserved for header comment (12:1-12:3)" +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 sign are reserved for header comment (13:1-13:15)" +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 sign are reserved for header comment (14:1-14:85)" +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 sign are reserved for header comment (15:1-15:87)" +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 sign are reserved for header comment (16:1-16:86)" +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 sign are reserved for header comment (17:1-17:84)" +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 sign are reserved for header comment (18:1-18:86)" +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 sign are reserved for header comment (19:1-19:62)" +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 sign are reserved for header comment (5:1-5:35)" +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 sign are reserved for header comment (6:1-6:3)" +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 sign are reserved for header comment (7:1-7:92)" +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 sign are reserved for header comment (8:1-8:3)" +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 sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -42218,12 +42233,12 @@ 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 sign are reserved for header comment (20:3-20:147)" +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 sign are reserved for header comment (62:3-62:14)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (62:3-62:14)" [[concerns]] kind = "LintWarning" @@ -42363,12 +42378,12 @@ 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 sign are reserved for header comment (28:3-28:147)" +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 sign are reserved for header comment (70:3-70:14)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (70:3-70:14)" [[concerns]] kind = "LintWarning" @@ -42443,77 +42458,77 @@ message = "[v1::W007::Spacing/Low] missing newline at the end of the file (96:2- [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (10:1-10:3)" +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 sign are reserved for header comment (11:1-11:86)" +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 sign are reserved for header comment (12:1-12:48)" +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 sign are reserved for header comment (13:1-13:3)" +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 sign are reserved for header comment (14:1-14:15)" +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 sign are reserved for header comment (15:1-15:85)" +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 sign are reserved for header comment (16:1-16:87)" +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 sign are reserved for header comment (17:1-17:86)" +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 sign are reserved for header comment (18:1-18:84)" +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 sign are reserved for header comment (19:1-19:86)" +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 sign are reserved for header comment (20:1-20:62)" +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 sign are reserved for header comment (6:1-6:35)" +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 sign are reserved for header comment (7:1-7:3)" +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 sign are reserved for header comment (8:1-8:86)" +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 sign are reserved for header comment (9:1-9:3)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (9:1-9:3)" [[concerns]] kind = "LintWarning" @@ -49473,22 +49488,22 @@ message = "[v1::W007::Spacing/Low] missing newline at the end of the file (230:2 [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (50:5-50:57)" +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 sign are reserved for header comment (51:5-51:37)" +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 sign are reserved for header comment (52:5-52:51)" +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 sign are reserved for header comment (72:5-72:33)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (72:5-72:33)" [[concerns]] kind = "LintWarning" @@ -49683,12 +49698,12 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within workflo [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (28:9-28:88)" +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 sign are reserved for header comment (44:9-44:88)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (44:9-44:88)" [[concerns]] kind = "LintWarning" @@ -50008,22 +50023,22 @@ message = "[v1::W007::Spacing/Low] multiple empty lines at the end of file (234: [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W010::Style/Low] double pound sign are reserved for header comment (51:5-51:57)" +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 sign are reserved for header comment (52:5-52:37)" +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 sign are reserved for header comment (53:5-53:51)" +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 sign are reserved for header comment (73:5-73:33)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (73:5-73:33)" [[concerns]] kind = "LintWarning" @@ -51123,27 +51138,27 @@ 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] header comments without a double pound sign (1:1-1:34)" +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] header comments without a double pound sign (2:1-2:29)" +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] header comments without a double pound sign (3:1-3:85)" +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] header comments without a double pound sign (4:1-4:114)" +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] header comments without a double pound sign (5:1-5:78)" +message = "[v1::W010::Style/Low] preamble comment without a double pound sign (5:1-5:78)" [[concerns]] kind = "LintWarning" @@ -51200,11 +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" @@ -52233,22 +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" @@ -52258,7 +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" @@ -52278,37 +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" @@ -52318,52 +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 (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 (1029:9-1029:29)" +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 (1109:9-1109:29)" +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 (734:9-734:29)" +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 (781:9-781:29)" +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: deuterostome_db (984:9-984:29)" +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: diamond_args (598:9-598:28)" +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 (1034:9-1034:31)" +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 (1072:9-1072:31)" +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 (1116:9-1116:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1120:9-1120:31)" [[concerns]] kind = "LintWarning" @@ -52373,17 +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" @@ -52438,42 +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" @@ -52483,17 +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" @@ -52548,12 +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" @@ -52568,47 +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" @@ -52618,18 +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" @@ -52648,122 +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" @@ -52773,7 +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" @@ -52783,27 +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" @@ -52823,7 +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" @@ -52833,17 +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" @@ -52853,247 +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 (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 (1111:9-1111:29)" +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 (736:9-736:29)" +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 (783:9-783:29)" +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_blacklist (986:9-986:29)" +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 (1030:9-1030:29)" +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 (1110:9-1110:29)" +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 (735:9-735:29)" +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 (782:9-782:29)" +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: taxon_whitelist (985:9-985:29)" +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 (1032:9-1032:40)" +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 (1113:9-1113:40)" +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 (737:9-737:40)" +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 (784:9-784:40)" +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_deuterostome_filter (987:9-987:40)" +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 (1033:9-1033:36)" +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 (1114:9-1114:36)" +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 (738:9-738:36)" +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 (785:9-785:36)" +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 task: use_taxon_whitelist (988:9-988:36)" +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: accession2taxid_db (1288:9-1288:32)" +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: deuterostome_db (1292:9-1292:29)" +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_args (1300:9-1300:43)" +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_db (1299:9-1299:27)" +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: diamond_local_db_path (1285:9-1285:36)" +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: docker_image_id (1268:9-1268:31)" +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: guppy_basecaller_setting (1275:9-1275:48)" +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: input_fastq (1272:9-1272:25)" +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: library_type (1274:9-1274:36)" +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: lineage_db (1287:9-1287:24)" +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: min_read_length (1291:9-1291:33)" +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_args (1296:9-1296:61)" +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_db (1295:9-1295:28)" +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_local_db_path (1284:9-1284:37)" +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: minimap2_prefix (1297:9-1297:41)" +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_host_db (1279:9-1279:29)" +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: minimap_human_db (1280:9-1280:30)" +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: nt_info_db (1293:9-1293:24)" +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: polishing_iterations (1282:9-1282:37)" +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: s3_wd_uri (1270:9-1270:26)" +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: subsample_depth (1277:9-1277:38)" +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_blacklist (1289:9-1289:29)" +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: taxon_whitelist (1290:9-1290:113)" +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_deuterostome_filter (1302:9-1302:47)" +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::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: 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 (1023:6-1023:24)" +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 (1026:14-1026:30)" +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 (1068:6-1068:27)" +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 (1098:6-1098:30)" +message = "[v1::W006::Naming/Low] identifier must be snake case (1072:6-1072:27)" [[concerns]] kind = "LintWarning" @@ -53103,7 +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" @@ -53113,77 +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" @@ -53253,17 +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" @@ -53273,132 +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" @@ -55058,27 +55098,27 @@ 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 sign are reserved for header comment (710:1-710:100)" +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 sign are reserved for header comment (711:1-711:98)" +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 sign are reserved for header comment (712:1-712:99)" +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 sign are reserved for header comment (713:1-713:96)" +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 sign are reserved for header comment (714:1-714:100)" +message = "[v1::W010::Style/Low] double pound signs are reserved for preamble comments (714:1-714:100)" [[concerns]] kind = "LintWarning" @@ -55133,57 +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" @@ -55198,22 +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" @@ -55228,7 +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" @@ -55238,32 +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" @@ -55283,12 +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" @@ -55298,7 +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" @@ -55333,17 +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" @@ -55353,22 +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" @@ -55378,17 +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 (171:9-171:22)" +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 (227:9-227:22)" +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 (231:9-231:22)" [[concerns]] kind = "LintWarning" @@ -55418,7 +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" @@ -55428,17 +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" @@ -55458,257 +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 (209:14-209:28)" +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 (219:6-219:24)" +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 (221:14-221:21)" +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 (225:14-225:29)" +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 (231:16-231:25)" +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 (264:14-264:28)" +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 (278:12-278:21)" +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 (286:10-286:28)" +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 (295:11-295:33)" +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 (298:11-298:33)" +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 (299:12-299:23)" +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 (301:12-301:25)" +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 (303:12-303:27)" +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 (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" @@ -55733,47 +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" @@ -55820,6 +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" @@ -57258,17 +57328,17 @@ 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] header comments without a double pound sign (2:1-2:2)" +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] header comments without a double pound sign (3:1-3:31)" +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] header comments without a double pound sign (4:1-4:50)" +message = "[v1::W010::Style/Low] preamble comment without a double pound sign (4:1-4:50)" [[concerns]] kind = "LintWarning" @@ -57923,12 +57993,12 @@ message = "[v1::W007::Spacing/Low] missing newline at the end of the file (108:2 [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" -message = "[v1::W010::Style/Low] header comments without a double pound sign (1:1-1:31)" +message = "[v1::W010::Style/Low] preamble comment without a double pound sign (1:1-1:31)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" -message = "[v1::W010::Style/Low] header comments without a double pound sign (2:1-2:50)" +message = "[v1::W010::Style/Low] preamble comment without a double pound sign (2:1-2:50)" [[concerns]] kind = "LintWarning" @@ -57963,12 +58033,12 @@ message = "[v1::W007::Spacing/Low] multiple empty lines at the end of file (126: [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-variant-calling.wdl" -message = "[v1::W010::Style/Low] header comments without a double pound sign (1:1-1:31)" +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-variant-calling.wdl" -message = "[v1::W010::Style/Low] header comments without a double pound sign (2:1-2:50)" +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 ef167c73..afecc6b2 100644 --- a/RULES.md +++ b/RULES.md @@ -24,7 +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] | -| `header_comment` | `v1::W010` | Style | [`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/lint-rules.md b/lint-rules.md index b27be5d0..41c0433c 100644 --- a/lint-rules.md +++ b/lint-rules.md @@ -14,7 +14,7 @@ At the time of writing (January 2024), we consider all rules herein to be up for ### `version_declaration_placement` -The WDL version declaration is required for any v1 WDL document to be parsed. A missing version declaration will result in a validation error. However an incorrect placement of the decleration will be considered a lint warning. The version decleration should be the very first line in the document, unless there are header comments. In which case, there should be a blank line between the header and the version declaration. There should _always_ be a blank line following the version declaration. +The WDL version declaration is required for any v1 WDL document to be parsed. A missing version declaration will result in a validation error. However an incorrect placement of the decleration will be considered a lint warning. The version decleration should be the very first line in the document, unless there are preamble comments. In which case, there should be a blank line between the preamble and the version declaration. There should _always_ be a blank line following the version declaration. **Group**: `spacing` @@ -381,13 +381,13 @@ Bad: Int z = x + y# NO spaces between code and comment is hard to read. ``` -### `header_comment` +### `preamble_comment` -Full line comments which start with a double-pound-sign (`##`) are given special treatment. They are called header-comments, and **should only be used at the very beginning of a file**. These special comments are meant as a place for documentation that doesn't belong in any of the language-supported meta sections. This is often whole file documentation or documentation for structs contained in the file. +Full line comments which start with a double-pound-sign (`##`) are given special treatment. They are called preamble comments, and **should only be used at the very beginning of a file**. These special comments are meant as a place for documentation that doesn't belong in any of the language-supported meta sections. This is often whole file documentation or documentation for structs contained in the file. -`sprocket doc` is under active development at the time of writing. This tool will auto-document any WDL file in Markdown. Header-comments found by `sprocket doc` will be re-written in the output `.md` files (without the `##` prefix). Arbitrary and multi-line Markdown constructions will be preserved and rendered. +`sprocket doc` is under active development at the time of writing. This tool will auto-document any WDL file in Markdown. Preamble comments found by `sprocket doc` will be re-written in the output `.md` files (without the `##` prefix). Arbitrary and multi-line Markdown constructions will be preserved and rendered. -Header comments may only precede the version declaration. They are not allowed anywhere else. +Preamble comments may only precede the version declaration. They are not allowed anywhere else. ### `double_quotes` diff --git a/wdl-grammar/CHANGELOG.md b/wdl-grammar/CHANGELOG.md index ea2fdbfa..c5c1d019 100644 --- a/wdl-grammar/CHANGELOG.md +++ b/wdl-grammar/CHANGELOG.md @@ -14,8 +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 `header_comment` rule for header comment formatting (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 579c39dc..30709687 100644 --- a/wdl-grammar/src/v1.rs +++ b/wdl-grammar/src/v1.rs @@ -23,7 +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) | -//! | `header_comment` | `v1::W010` | Style | [Link](lint::HeaderComment) | +//! | `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 741e973c..de07d32e 100644 --- a/wdl-grammar/src/v1/lint.rs +++ b/wdl-grammar/src/v1/lint.rs @@ -2,19 +2,19 @@ use pest::iterators::Pair; -mod header_comment; mod missing_runtime_block; mod mixed_indentation; mod newline_eof; mod no_curly_commands; +mod preamble_comment; mod snake_case; mod whitespace; -pub use header_comment::HeaderComment; 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; @@ -34,6 +34,6 @@ pub fn rules<'a>() -> Vec HeaderComment { - /// Creates a warning for header comments without double pound sign +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>>, @@ -28,7 +28,7 @@ impl<'a> HeaderComment { .code(self.code()) .level(lint::Level::Low) .group(self.group()) - .subject("header comments without a double pound sign") + .subject("preamble comment without a double pound sign") .body( "Header comments are full line comments before the version declaration and they \ start with a double pound sign.", @@ -39,8 +39,8 @@ impl<'a> HeaderComment { .unwrap() } - /// Creates a warning for header comments after version declaration - fn header_comment_after_version(&self, location: Location) -> lint::Warning + /// 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>>, { @@ -48,10 +48,10 @@ impl<'a> HeaderComment { .code(self.code()) .level(lint::Level::Low) .group(self.group()) - .subject("double pound sign are reserved for header comment") + .subject("double pound signs are reserved for preamble comments") .body( - "Only full line comment before version declaration should start with a double \ - pound sign.", + "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.") @@ -60,7 +60,7 @@ impl<'a> HeaderComment { } } -impl<'a> Rule<&Pair<'a, v1::Rule>> for HeaderComment { +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() @@ -73,26 +73,26 @@ impl<'a> Rule<&Pair<'a, v1::Rule>> for HeaderComment { fn check(&self, tree: &Pair<'a, v1::Rule>) -> lint::Result { let mut warnings = VecDeque::new(); - let mut is_header = true; + let mut is_preamble = true; for node in tree.clone().into_inner().flatten() { match node.as_rule() { v1::Rule::version => { - is_header = false; + is_preamble = false; } v1::Rule::COMMENT => { // Catches missing double pound sign - if is_header & !node.as_str().starts_with("##") { + 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 header comment after version declaration - if !is_header & node.as_str().starts_with("##") { + // 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.header_comment_after_version(location)); + warnings.push_back(self.preamble_comment_after_version(location)); } } _ => {} @@ -120,7 +120,7 @@ mod tests { use crate::v1::Rule; #[test] - fn it_catches_badly_formatted_header_comment() -> Result<(), Box> { + fn it_catches_badly_formatted_preamble_comment() -> Result<(), Box> { let tree = Parser::parse( Rule::document, r#"# a comment @@ -130,17 +130,17 @@ version 1.0 .next() .unwrap(); - let warnings = HeaderComment.check(&tree)?.unwrap(); + let warnings = PreambleComment.check(&tree)?.unwrap(); assert_eq!(warnings.len(), 1); assert_eq!( warnings.first().to_string(), - "[v1::W010::Style/Low] header comments without a double pound sign (1:1-1:12)" + "[v1::W010::Style/Low] preamble comment without a double pound sign (1:1-1:12)" ); Ok(()) } #[test] - fn it_catches_header_comment_after_version() -> Result<(), Box> { + fn it_catches_preamble_comment_after_version() -> Result<(), Box> { let tree = Parser::parse( Rule::document, r#"## a comment @@ -152,17 +152,19 @@ version 1.0 .next() .unwrap(); - let warnings = HeaderComment.check(&tree)?.unwrap(); + let warnings = PreambleComment.check(&tree)?.unwrap(); assert_eq!(warnings.len(), 1); assert_eq!( warnings.first().to_string(), - "[v1::W010::Style/Low] double pound sign are reserved for header comment (4:1-4:19)" + "[v1::W010::Style/Low] double pound signs are reserved for preamble comments \ + (4:1-4:19)" ); Ok(()) } #[test] - fn it_ignores_a_properly_formatted_header_comment() -> Result<(), Box> { + fn it_ignores_a_properly_formatted_preamble_comment() -> Result<(), Box> + { let tree = Parser::parse( Rule::document, r#"## a comment @@ -171,7 +173,7 @@ version 1.0 )? .next() .unwrap(); - let warnings = HeaderComment.check(&tree)?; + let warnings = PreambleComment.check(&tree)?; assert!(warnings.is_none()); Ok(()) } From da696b66d1b8c2f929477875028e7dc9cec301ce Mon Sep 17 00:00:00 2001 From: Andrew Thrasher Date: Mon, 13 May 2024 10:13:22 -0400 Subject: [PATCH 4/6] Update wdl-grammar/src/v1/lint/preamble_comment.rs --- wdl-grammar/src/v1/lint/preamble_comment.rs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-grammar/src/v1/lint/preamble_comment.rs b/wdl-grammar/src/v1/lint/preamble_comment.rs index f61e245e..b13af2a1 100644 --- a/wdl-grammar/src/v1/lint/preamble_comment.rs +++ b/wdl-grammar/src/v1/lint/preamble_comment.rs @@ -30,7 +30,7 @@ impl<'a> PreambleComment { .group(self.group()) .subject("preamble comment without a double pound sign") .body( - "Header comments are full line comments before the version declaration and they \ + "Preamble comments are full line comments before the version declaration and they \ start with a double pound sign.", ) .push_location(location) From 8966231d52f10c10e427d1350df7e08e6b0d1ee8 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 13 May 2024 10:14:05 -0400 Subject: [PATCH 5/6] Update wdl-grammar/src/v1/lint/preamble_comment.rs Co-authored-by: Andrew Thrasher --- wdl-grammar/src/v1/lint/preamble_comment.rs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-grammar/src/v1/lint/preamble_comment.rs b/wdl-grammar/src/v1/lint/preamble_comment.rs index b13af2a1..4e0ae8bb 100644 --- a/wdl-grammar/src/v1/lint/preamble_comment.rs +++ b/wdl-grammar/src/v1/lint/preamble_comment.rs @@ -1,4 +1,4 @@ -//! Preamble comments are full line comments starting with a double pound sign +//! Preamble comments are full line comments starting with a double pound sign and must occur before the version declaration use std::collections::VecDeque; From daad4764d4c03cf1dc40ade276d7b2a31803a863 Mon Sep 17 00:00:00 2001 From: Andrew Thrasher Date: Mon, 13 May 2024 10:21:16 -0400 Subject: [PATCH 6/6] chore: cargo fmt --- wdl-grammar/src/v1/lint/preamble_comment.rs | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/wdl-grammar/src/v1/lint/preamble_comment.rs b/wdl-grammar/src/v1/lint/preamble_comment.rs index 4e0ae8bb..5c8c023f 100644 --- a/wdl-grammar/src/v1/lint/preamble_comment.rs +++ b/wdl-grammar/src/v1/lint/preamble_comment.rs @@ -1,4 +1,5 @@ -//! Preamble comments are full line comments starting with a double pound sign and must occur before the version declaration +//! Preamble comments are full line comments starting with a double pound sign +//! and must occur before the version declaration use std::collections::VecDeque;