Arena.toml

[repositories."getwilds/ww-fastq-to-cram"]
identifier = "getwilds/ww-fastq-to-cram"
commit_hash = "2d1e1989a57402642c06d15f4b623ac66fd9ed7d"

[repositories."getwilds/ww-star-deseq2"]
identifier = "getwilds/ww-star-deseq2"
commit_hash = "eb2efc50a94fd9e9579775acbf776d20ea2da0d1"

[repositories."getwilds/ww-vc-trio"]
identifier = "getwilds/ww-vc-trio"
commit_hash = "c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2"

[repositories."stjudecloud/workflows"]
identifier = "stjudecloud/workflows"
commit_hash = "8377299f9d171af316f06570eedcd12e39600d72"
filters = ["/template/task-templates.wdl"]

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:10:34: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L10"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:127:60: note[BlankLinesBetweenElements]: extra blank line(s) found"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L127"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:129:5: note[MatchingParameterMeta]: task `FastqToUnmappedBam` has an extraneous parameter metadata key named `unmapped_bam`"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L129"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:133:46: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L133"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:134:6: note[MissingMetas]: task `ValidateCram` is missing a `meta` section"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L134"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:134:6: note[SectionOrdering]: sections are not in order for task `ValidateCram`"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L134"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:134:6: warning[SnakeCase]: task name `ValidateCram` is not snake_case"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L134"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:14:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L14"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:14:21: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L14"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:15:22: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L15"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:163:60: note[BlankLinesBetweenElements]: extra blank line(s) found"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L163"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:165:5: note[MatchingParameterMeta]: task `ValidateCram` has an extraneous parameter metadata key named `validation`"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L165"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:16:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L16"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:16:23: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L16"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:170:6: note[MissingMetas]: task `MergeBamsToCram` is missing a `meta` section"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L170"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:170:6: note[SectionOrdering]: sections are not in order for task `MergeBamsToCram`"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L170"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:170:6: warning[SnakeCase]: task name `MergeBamsToCram` is not snake_case"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L170"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:17:28: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L17"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:180:32: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L180"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:18:35: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L18"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:1:12: note[VersionFormatting]: expected exactly one blank line after the version statement"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L1"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:200:67: note[BlankLinesBetweenElements]: extra blank line(s) found"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L200"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:202:5: note[MatchingParameterMeta]: task `MergeBamsToCram` has an extraneous parameter metadata key named `cram`"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L202"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:203:5: note[MatchingParameterMeta]: task `MergeBamsToCram` has an extraneous parameter metadata key named `crai`"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L203"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:205:1: note[EndingNewline]: missing newline at the end of the file"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L205"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:23:10: note[MissingMetas]: workflow `PairedFastqsToUnmappedCram` is missing a `meta` section"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L23"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:23:10: note[SectionOrdering]: sections are not in order for workflow `PairedFastqsToUnmappedCram`"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L23"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:23:10: warning[SnakeCase]: workflow name `PairedFastqsToUnmappedCram` is not snake_case"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L23"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:31:36: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L31"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:34:104: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L34"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:34:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L34"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:34:46: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L34"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:35:112: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L35"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:35:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L35"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:35:33: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L35"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:44:20: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L44"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:46:7: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L46"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:48:116: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L48"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:48:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L48"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:48:28: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L48"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:53:19: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L53"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:56:25: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L56"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:56:67: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L56"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:57:13: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L57"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:58:22: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L58"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:60:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L60"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:62:5: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L62"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:64:3: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L64"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:72:94: note[BlankLinesBetweenElements]: extra blank line(s) found"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L72"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:74:5: note[MatchingParameterMeta]: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `unmapped_crams`"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L74"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:75:5: note[MatchingParameterMeta]: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `unmapped_cram_indexes`"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L75"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:76:5: note[MatchingParameterMeta]: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `validation`"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L76"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:78:3: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L78"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:83:6: note[MissingMetas]: task `FastqToUnmappedBam` is missing a `meta` section"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L83"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:83:6: note[SectionOrdering]: sections are not in order for task `FastqToUnmappedBam`"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L83"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:83:6: warning[SnakeCase]: task name `FastqToUnmappedBam` is not snake_case"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L83"

[[diagnostics]]
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message = "ww-fastq-to-cram.wdl:8:24: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L8"

[[diagnostics]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
message = "ww-fastq-to-cram.wdl:8:42: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L8"

[[diagnostics]]
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message = "ww-fastq-to-cram.wdl:9:34: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-fastq-to-cram/blob/2d1e1989a57402642c06d15f4b623ac66fd9ed7d/ww-fastq-to-cram.wdl/#L9"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:127:13: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L127"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:133:6: note[MissingMetas]: task `CollapseGTF` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L133"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:133:6: warning[SnakeCase]: task name `CollapseGTF` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L133"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:152:13: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L152"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:158:6: note[MissingMetas]: task `STARalignTwoPass` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L158"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:158:6: warning[SnakeCase]: task name `STARalignTwoPass` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L158"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:15:10: note[MissingMetas]: workflow `STAR2Pass` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L15"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:15:10: warning[SnakeCase]: workflow name `STAR2Pass` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L15"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:192:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L192"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:205:10: warning[SnakeCase]: output name `geneCounts` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L205"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:209:10: warning[SnakeCase]: output name `SJout` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L209"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:213:13: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L213"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:219:6: note[MissingMetas]: task `RNASeQC` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L219"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:219:6: warning[SnakeCase]: task name `RNASeQC` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L219"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:243:13: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L243"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:27:21: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L27"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:32:24: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L32"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:35:40: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L35"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:39:28: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L39"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:45:44: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L45"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:48:19: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L48"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:53:31: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L53"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:58:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L58"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:59:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L59"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:5:10: warning[SnakeCase]: struct member name `R1` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L5"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:60:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L60"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:60:17: warning[SnakeCase]: output name `output_geneCounts` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L60"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:61:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L61"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:62:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L62"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:63:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L63"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:64:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L64"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:64:17: warning[SnakeCase]: output name `output_SJ` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L64"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:65:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L65"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:69:6: note[MissingMetas]: task `DownloadReference` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L69"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:69:6: warning[SnakeCase]: task name `DownloadReference` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L69"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:6:10: warning[SnakeCase]: struct member name `R2` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L6"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:73:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L73"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:74:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L74"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:83:52: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L83"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:88:13: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L88"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:94:6: note[MissingMetas]: task `BuildSTARIndex` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L94"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:94:6: warning[SnakeCase]: task name `BuildSTARIndex` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L94"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:98:9: warning[SnakeCase]: input name `sjdbOverhang` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L98"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:99:9: warning[SnakeCase]: input name `genomeSAindexNbases` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/eb2efc50a94fd9e9579775acbf776d20ea2da0d1/ww-star-deseq2.wdl/#L99"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:106:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L106"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:109:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L109"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:110:26: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L110"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:115:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L115"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:118:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L118"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:119:33: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L119"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:132:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L132"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:135:22: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L135"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:136:13: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L136"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:141:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L141"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:144:28: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L144"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:145:13: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L145"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:151:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L151"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:154:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L154"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:155:27: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L155"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:166:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L166"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:169:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L169"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:16:3: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L16"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:170:28: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L170"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:17:10: note[MissingMetas]: workflow `ww_vc_trio` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L17"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:181:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L181"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:184:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L184"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:185:27: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L185"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:18:3: note[InputSorting]: input not sorted"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L18"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:195:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L195"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:198:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L198"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:199:34: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L199"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:19:10: warning[SnakeCase]: input name `batchFile` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L19"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:1:12: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L1"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:1:12: note[VersionFormatting]: expected exactly one blank line after the version statement"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L1"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:205:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L205"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:208:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L208"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:209:37: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L209"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:20:10: warning[SnakeCase]: input name `bedLocation` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L20"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:215:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L215"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:217:1: note[Whitespace]: line contains only whitespace"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L217"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:218:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L218"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:219:40: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L219"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:225:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L225"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:228:32: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L228"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:234:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L234"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:236:18: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L236"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:236:5: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L236"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:238:3: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L238"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:240:76: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L240"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:242:17: warning[SnakeCase]: output name `GATK_vcf` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L242"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:243:17: warning[SnakeCase]: output name `SAM_vcf` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L243"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:244:17: warning[SnakeCase]: output name `Mutect_Vcf` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L244"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:245:17: warning[SnakeCase]: output name `Mutect_VcfIndex` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L245"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:246:17: warning[SnakeCase]: output name `Mutect_AnnotatedVcf` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L246"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:247:17: warning[SnakeCase]: output name `Mutect_AnnotatedTable` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L247"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:248:17: warning[SnakeCase]: output name `GATK_annotated_vcf` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L248"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:249:17: warning[SnakeCase]: output name `GATK_annotated` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L249"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:250:17: warning[SnakeCase]: output name `SAM_annotated_vcf` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L250"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:251:17: warning[SnakeCase]: output name `SAM_annotated` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L251"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:252:17: warning[SnakeCase]: output name `panelQC` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L252"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:253:17: warning[SnakeCase]: output name `PicardQC` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L253"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:254:17: warning[SnakeCase]: output name `PicardQCpertarget` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L254"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:255:17: warning[SnakeCase]: output name `consensusVariants` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L255"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:257:3: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L257"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:25:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L25"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:262:6: note[MissingMetas]: task `annovar` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L262"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:264:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L264"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:26:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L26"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:27:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L27"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:282:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L282"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:286:10: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L286"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:287:10: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L287"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:298:6: note[MissingMetas]: task `ApplyBaseRecalibrator` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L298"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:298:6: warning[SnakeCase]: task name `ApplyBaseRecalibrator` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L298"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:299:3: note[InputSorting]: input not sorted"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L299"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:300:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L300"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:301:19: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L301"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:302:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L302"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:304:10: warning[SnakeCase]: input name `dbSNP_vcf` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L304"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:305:10: warning[SnakeCase]: input name `dbSNP_vcf_index` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L305"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:306:17: warning[SnakeCase]: input name `known_indels_sites_VCFs` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L306"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:336:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L336"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:342:10: warning[SnakeCase]: output name `sortOrder` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L342"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:34:10: warning[SnakeCase]: input name `dbSNP_vcf` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L34"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:353:6: note[MissingMetas]: task `bcftoolsMpileup` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L353"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:353:6: warning[SnakeCase]: task name `bcftoolsMpileup` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L353"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:354:3: note[InputSorting]: input not sorted"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L354"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:355:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L355"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:356:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L356"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:35:10: warning[SnakeCase]: input name `dbSNP_vcf_index` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L35"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:362:10: warning[SnakeCase]: input name `dbSNP_vcf` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L362"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:36:17: warning[SnakeCase]: input name `known_indels_sites_VCFs` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L36"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:381:10: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L381"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:392:6: note[MissingMetas]: task `bedToolsQC` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L392"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:392:6: warning[SnakeCase]: task name `bedToolsQC` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L392"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:394:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L394"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:409:10: warning[SnakeCase]: output name `meanQC` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L409"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:40:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L40"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:40:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L40"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:420:6: note[MissingMetas]: task `BwaMem` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L420"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:420:6: warning[SnakeCase]: task name `BwaMem` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L420"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:421:3: note[InputSorting]: input not sorted"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L421"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:422:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L422"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:441:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L441"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:445:10: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L445"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:456:6: note[MissingMetas]: task `CollectHsMetrics` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L456"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:456:6: warning[SnakeCase]: task name `CollectHsMetrics` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L456"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:457:3: note[InputSorting]: input not sorted"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L457"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:458:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L458"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:45:17: warning[SnakeCase]: private declaration name `batchInfo` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L45"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:46:3: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L46"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:47:10: warning[SnakeCase]: private declaration name `GATKDocker` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L47"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:481:10: warning[SnakeCase]: output name `picardMetrics` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L481"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:482:10: warning[SnakeCase]: output name `picardPerTarget` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L482"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:48:10: warning[SnakeCase]: private declaration name `bwaDocker` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L48"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:492:6: note[MissingMetas]: task `consensusProcessingR` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L492"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:492:6: warning[SnakeCase]: task name `consensusProcessingR` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L492"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:494:10: warning[SnakeCase]: input name `GATKVars` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L494"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:495:10: warning[SnakeCase]: input name `SAMVars` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L495"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:496:10: warning[SnakeCase]: input name `MutectVars` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L496"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:49:10: warning[SnakeCase]: private declaration name `bedtoolsDocker` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L49"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:49:53: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L49"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:4:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L4"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:503:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L503"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:507:10: warning[SnakeCase]: output name `consensusTSV` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L507"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:50:10: warning[SnakeCase]: private declaration name `bcftoolsDocker` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L50"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:518:6: note[MissingMetas]: task `HaplotypeCaller` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L518"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:518:6: warning[SnakeCase]: task name `HaplotypeCaller` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L518"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:519:3: note[InputSorting]: input not sorted"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L519"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:51:10: warning[SnakeCase]: private declaration name `annovarDocker` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L51"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:520:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L520"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:521:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L521"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:527:10: warning[SnakeCase]: input name `dbSNP_vcf` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L527"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:52:10: warning[SnakeCase]: private declaration name `RDocker` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L52"

[[diagnostics]]
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message = "ww-vc-trio.wdl:546:10: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L546"

[[diagnostics]]
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message = "ww-vc-trio.wdl:547:10: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L547"

[[diagnostics]]
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message = "ww-vc-trio.wdl:54:7: warning[SnakeCase]: private declaration name `bwaThreads` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L54"

[[diagnostics]]
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message = "ww-vc-trio.wdl:558:6: note[MissingMetas]: task `MergeBamAlignment` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L558"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:558:6: warning[SnakeCase]: task name `MergeBamAlignment` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L558"

[[diagnostics]]
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message = "ww-vc-trio.wdl:559:3: note[InputSorting]: input not sorted"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L559"

[[diagnostics]]
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permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L56"

[[diagnostics]]
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permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L571"

[[diagnostics]]
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message = "ww-vc-trio.wdl:57:17: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L57"

[[diagnostics]]
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message = "ww-vc-trio.wdl:585:10: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L585"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:596:6: note[MissingMetas]: task `Mutect2TumorOnly` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L596"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:596:6: warning[SnakeCase]: task name `Mutect2TumorOnly` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L596"

[[diagnostics]]
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message = "ww-vc-trio.wdl:597:3: note[InputSorting]: input not sorted"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L597"

[[diagnostics]]
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message = "ww-vc-trio.wdl:598:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L598"

[[diagnostics]]
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message = "ww-vc-trio.wdl:599:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L599"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:605:10: warning[SnakeCase]: input name `genomeReference` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L605"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:606:10: warning[SnakeCase]: input name `genomeReferenceIndex` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L606"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:61:16: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L61"

[[diagnostics]]
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message = "ww-vc-trio.wdl:631:10: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L631"

[[diagnostics]]
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message = "ww-vc-trio.wdl:632:10: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L632"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:643:6: note[MissingMetas]: task `SamToFastq` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L643"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:643:6: warning[SnakeCase]: task name `SamToFastq` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L643"

[[diagnostics]]
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message = "ww-vc-trio.wdl:645:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L645"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:64:12: warning[SnakeCase]: private declaration name `sampleName` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L64"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:650:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L650"

[[diagnostics]]
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message = "ww-vc-trio.wdl:650:3: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L650"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:65:12: warning[SnakeCase]: private declaration name `molecularID` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L65"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:669:10: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L669"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:66:10: warning[SnakeCase]: private declaration name `sampleBam` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L66"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:680:6: note[MissingMetas]: task `SortBed` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L680"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:680:6: warning[SnakeCase]: task name `SortBed` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L680"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:709:6: note[MissingMetas]: task `MarkDuplicates` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L709"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:709:6: warning[SnakeCase]: task name `MarkDuplicates` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L709"

[[diagnostics]]
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message = "ww-vc-trio.wdl:711:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L711"

[[diagnostics]]
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message = "ww-vc-trio.wdl:717:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L717"

[[diagnostics]]
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message = "ww-vc-trio.wdl:717:3: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L717"

[[diagnostics]]
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message = "ww-vc-trio.wdl:718:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L718"

[[diagnostics]]
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message = "ww-vc-trio.wdl:718:3: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L718"

[[diagnostics]]
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message = "ww-vc-trio.wdl:719:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L719"

[[diagnostics]]
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message = "ww-vc-trio.wdl:719:3: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L719"

[[diagnostics]]
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message = "ww-vc-trio.wdl:71:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L71"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:72:22: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L72"

[[diagnostics]]
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message = "ww-vc-trio.wdl:732:10: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L732"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:733:10: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L733"

[[diagnostics]]
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message = "ww-vc-trio.wdl:744:87: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L744"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:745:6: note[MissingMetas]: task `SortSam` is missing both `meta` and `parameter_meta` sections"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L745"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:745:6: warning[SnakeCase]: task name `SortSam` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L745"

[[diagnostics]]
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message = "ww-vc-trio.wdl:747:10: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L747"

[[diagnostics]]
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message = "ww-vc-trio.wdl:763:10: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L763"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:76:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L76"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:771:2: note[EndingNewline]: multiple empty lines at the end of file"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L771"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:79:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L79"

[[diagnostics]]
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message = "ww-vc-trio.wdl:7:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L7"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:80:18: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L80"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:94:18: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L94"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:96:1: note[Whitespace]: line contains only whitespace"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L96"

[[diagnostics]]
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message = "ww-vc-trio.wdl:97:5: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L97"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:98:29: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L98"

[[diagnostics]]
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permalink = "https://github.com/stjudecloud/workflows/blob/8377299f9d171af316f06570eedcd12e39600d72/workflows/rnaseq/rnaseq-standard.wdl/#L38"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard.wdl"
message = "rnaseq-standard.wdl:47:28: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/8377299f9d171af316f06570eedcd12e39600d72/workflows/rnaseq/rnaseq-standard.wdl/#L47"