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 = "6d81ede0ad963115697c3f707f073177ddde7013"

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

[repositories."stjudecloud/workflows"]
identifier = "stjudecloud/workflows"
commit_hash = "43462b0c3beb0e5f6caaac58d236b75997bef61a"
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]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
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]]
document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl"
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:10:22: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L10"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:110:13: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L110"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:117:92: note[BlankLinesBetweenElements]: extra blank line(s) found"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L117"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:119:5: note[MatchingParameterMeta]: task `FindFastqs` has an extraneous parameter metadata key named `r1_locs`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L119"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:120:5: note[MatchingParameterMeta]: task `FindFastqs` has an extraneous parameter metadata key named `r2_locs`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L120"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:125:6: note[MissingMetas]: task `ConcatenateFastQs` is missing a `meta` section"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L125"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:125:6: note[SectionOrdering]: sections are not in order for task `ConcatenateFastQs`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L125"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:125:6: warning[SnakeCase]: task name `ConcatenateFastQs` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L125"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:126:3: note[InputSorting]: input not sorted"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L126"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:133:15: note[DoubleQuotes]: string defined with single quotes"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L133"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:134:15: note[DoubleQuotes]: string defined with single quotes"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L134"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:143:13: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L143"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:151:61: note[BlankLinesBetweenElements]: extra blank line(s) found"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L151"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:153:5: note[MatchingParameterMeta]: task `ConcatenateFastQs` has an extraneous parameter metadata key named `r1fastq`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L153"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:154:5: note[MatchingParameterMeta]: task `ConcatenateFastQs` has an extraneous parameter metadata key named `r2fastq`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L154"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:159:6: note[MissingMetas]: task `STARalignTwoPass` is missing a `meta` section"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L159"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:159:6: note[SectionOrdering]: sections are not in order for task `STARalignTwoPass`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L159"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:159:6: warning[SnakeCase]: task name `STARalignTwoPass` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L159"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:183:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L183"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:192:10: warning[SnakeCase]: output name `geneCounts` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L192"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:196:10: warning[SnakeCase]: output name `SJout` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L196"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:1:12: note[VersionFormatting]: expected exactly one blank line after the version statement"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L1"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:200:13: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L200"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:210:58: note[BlankLinesBetweenElements]: extra blank line(s) found"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L210"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:212:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `bam`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L212"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:213:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `bai`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L213"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:214:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `geneCounts`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L214"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:215:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `log_final`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L215"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:216:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `log_progress`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L216"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:217:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `log`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L217"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:218:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `SJout`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L218"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:224:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L224"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:225:6: note[MissingMetas]: task `RNASeQC` is missing a `meta` section"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L225"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:225:6: note[SectionOrdering]: sections are not in order for task `RNASeQC`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L225"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:225:6: warning[SnakeCase]: task name `RNASeQC` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L225"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:23:22: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L23"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:244:13: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L244"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:253:64: note[BlankLinesBetweenElements]: extra blank line(s) found"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L253"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:255:5: note[MatchingParameterMeta]: task `RNASeQC` has an extraneous parameter metadata key named `rnaseqc_metrics`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L255"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:25:21: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L25"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:25:36: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L25"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:26:21: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L26"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:26:22: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L26"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:29:29: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L29"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:30:13: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L30"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:31:23: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L31"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:31:43: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L31"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:32:23: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L32"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:32:43: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L32"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:33:23: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L33"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:33:24: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L33"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:36:28: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L36"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:38:23: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L42"

[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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message = "ww-star-deseq2.wdl:50:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L50"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:51:6: note[BlankLinesBetweenElements]: extra blank line(s) found"
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[[diagnostics]]
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permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L53"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:53:5: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
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[[diagnostics]]
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permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L55"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:57:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
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[[diagnostics]]
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message = "ww-star-deseq2.wdl:58:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L58"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:59:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L59"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:59:17: warning[SnakeCase]: output name `output_geneCounts` is not snake_case"
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[[diagnostics]]
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message = "ww-star-deseq2.wdl:60:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
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[[diagnostics]]
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message = "ww-star-deseq2.wdl:61:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L61"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:62:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L62"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:63:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
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[[diagnostics]]
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message = "ww-star-deseq2.wdl:63:17: warning[SnakeCase]: output name `output_SJ` is not snake_case"
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[[diagnostics]]
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message = "ww-star-deseq2.wdl:64:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L64"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:6:10: note[MissingMetas]: workflow `STAR2Pass` is missing a `meta` section"
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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message = "ww-star-deseq2.wdl:71:100: note[BlankLinesBetweenElements]: extra blank line(s) found"
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[[diagnostics]]
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message = "ww-star-deseq2.wdl:73:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_bam`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L73"

[[diagnostics]]
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permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L74"

[[diagnostics]]
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[[diagnostics]]
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permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L76"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:77:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_log_progress`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L77"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:78:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_log`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L78"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:79:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_SJ`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L79"

[[diagnostics]]
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permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L7"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:80:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_rnaseqc`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L80"

[[diagnostics]]
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message = "ww-star-deseq2.wdl:82:3: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
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[[diagnostics]]
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message = "ww-star-deseq2.wdl:87:6: note[MissingMetas]: task `FindFastqs` is missing a `meta` section"
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[[diagnostics]]
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message = "ww-star-deseq2.wdl:87:6: note[SectionOrdering]: sections are not in order for task `FindFastqs`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L87"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:87:6: warning[SnakeCase]: task name `FindFastqs` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L87"

[[diagnostics]]
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permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L9"

[[diagnostics]]
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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]]
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permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L109"

[[diagnostics]]
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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]]
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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]]
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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]]
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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]]
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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]]
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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]]
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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"
message = "ww-vc-trio.wdl:528:10: warning[SnakeCase]: input name `dbSNP_index` is not snake_case"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L528"

[[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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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