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 = "a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a"
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:44:11: 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:53:9: 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:60:9: 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:26:9: 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:33:9: 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"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L38"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:39:32: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L39"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:40:16: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L40"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:41:16: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L41"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:42:19: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L42"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:42:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L42"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:45:19: note[CallInputSpacing]: call input not properly spaced"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L45"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:47:23: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L47"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:48:17: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L48"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:49:18: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L49"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:50:16: note[CallInputSpacing]: call inputs assignments must be surrounded with whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L50"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:50:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L50"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:51:6: note[BlankLinesBetweenElements]: extra blank line(s) found"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L51"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:53:18: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L53"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:53:5: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L53"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:55:3: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L55"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:57:17: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L57"

[[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/6d81ede0ad963115697c3f707f073177ddde7013/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/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L59"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:59:17: warning[SnakeCase]: output name `output_geneCounts` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L59"

[[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/6d81ede0ad963115697c3f707f073177ddde7013/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/6d81ede0ad963115697c3f707f073177ddde7013/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/6d81ede0ad963115697c3f707f073177ddde7013/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/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L63"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:63:17: warning[SnakeCase]: output name `output_SJ` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/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/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L64"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:6:10: note[MissingMetas]: workflow `STAR2Pass` is missing a `meta` section"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L6"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:6:10: note[SectionOrdering]: sections are not in order for workflow `STAR2Pass`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L6"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:6:10: warning[SnakeCase]: workflow name `STAR2Pass` is not snake_case"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L6"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:71:100: note[BlankLinesBetweenElements]: extra blank line(s) found"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L71"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
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]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:74:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_bai`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L74"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:75:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_gene_counts`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L75"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:76:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_log_final`"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L76"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
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]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
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]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
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]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:7:3: note[InputSorting]: input not sorted"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L7"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
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]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:82:3: note[CommentWhitespace]: in-line comments should be preceded by two spaces"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L82"

[[diagnostics]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:87:6: note[MissingMetas]: task `FindFastqs` is missing a `meta` section"
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: 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]]
document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl"
message = "ww-star-deseq2.wdl:9:25: note[Whitespace]: line contains trailing whitespace"
permalink = "https://github.com/getwilds/ww-star-deseq2/blob/6d81ede0ad963115697c3f707f073177ddde7013/ww-star-deseq2.wdl/#L9"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:106:9: 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:115:9: 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:132:9: 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:141:9: 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:151:9: 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:166:9: 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:181:9: 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:195:9: 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[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:205:9: 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:215:9: 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:225:9: 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:234:9: 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:2:1: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L2"

[[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"
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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:56:3: note[CommentWhitespace]: comment not sufficiently indented"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L56"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:571:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L571"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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:61:7: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L61"

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

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

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

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

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

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

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl: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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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:76:9: 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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:7:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2/ww-vc-trio.wdl/#L7"

[[diagnostics]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
message = "ww-vc-trio.wdl:80:18: note[CallInputSpacing]: call input not properly spaced"
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:94:9: 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]]
document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl"
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]]
document = "stjudecloud/workflows:/data_structures/flag_filter.wdl"
message = "flag_filter.wdl:119:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/data_structures/flag_filter.wdl/#L119"

[[diagnostics]]
document = "stjudecloud/workflows:/data_structures/flag_filter.wdl"
message = "flag_filter.wdl:155:6: note[BlankLinesBetweenElements]: extra blank line(s) found"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/data_structures/flag_filter.wdl/#L155"

[[diagnostics]]
document = "stjudecloud/workflows:/data_structures/read_group.wdl"
message = "read_group.wdl:107:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/data_structures/read_group.wdl/#L107"

[[diagnostics]]
document = "stjudecloud/workflows:/data_structures/read_group.wdl"
message = "read_group.wdl:159:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/data_structures/read_group.wdl/#L159"

[[diagnostics]]
document = "stjudecloud/workflows:/data_structures/read_group.wdl"
message = "read_group.wdl:192:47: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/data_structures/read_group.wdl/#L192"

[[diagnostics]]
document = "stjudecloud/workflows:/data_structures/read_group.wdl"
message = "read_group.wdl:444:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/data_structures/read_group.wdl/#L444"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:102:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L102"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:11:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L11"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:142:79: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L142"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:22:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L22"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:245:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L245"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:26:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L26"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:298:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L298"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:308:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L308"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:30:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L30"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:347:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L347"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:34:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L34"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:38:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L38"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:397:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L397"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:44:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L44"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:80:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L80"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:87:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L87"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:93:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L93"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/arriba.wdl"
message = "arriba.wdl:97:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/arriba.wdl/#L97"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:105:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L105"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:109:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L109"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:115:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L115"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:119:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L119"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:123:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L123"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:171:46: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L171"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:171:57: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L171"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:190:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L190"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:19:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L19"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:210:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L210"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:214:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L214"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:218:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L218"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:23:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L23"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:264:55: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L264"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:264:73: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L264"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:268:46: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L268"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:268:57: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L268"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:27:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L27"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:286:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L286"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:303:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L303"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:337:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L337"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/bwa.wdl"
message = "bwa.wdl:89:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/bwa.wdl/#L89"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:113:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L113"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:154:23: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L154"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:154:41: note[ExpressionSpacing]: multi-line if...then...else must have a preceding space"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L154"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:155:25: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L155"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:155:30: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L155"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:155:48: note[ExpressionSpacing]: multi-line if...then...else must have a preceding space"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L155"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:156:25: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L156"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:156:30: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L156"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:156:43: note[ExpressionSpacing]: multi-line if...then...else must have a preceding space"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L156"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:157:25: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L157"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:184:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L184"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:43:16: note[DisallowedInputName]: declaration identifier must be at least 3 characters"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L43"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:5:1: note[PreambleFormatting]: lint directives must come before preamble comments"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L5"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/cellranger.wdl"
message = "cellranger.wdl:95:14: note[DisallowedOutputName]: declaration identifier must be at least 3 characters"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/cellranger.wdl/#L95"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/deeptools.wdl"
message = "deeptools.wdl:19:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/deeptools.wdl/#L19"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/deeptools.wdl"
message = "deeptools.wdl:23:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/deeptools.wdl/#L23"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/deeptools.wdl"
message = "deeptools.wdl:70:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/deeptools.wdl/#L70"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/estimate.wdl"
message = "estimate.wdl:39:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/estimate.wdl/#L39"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/estimate.wdl"
message = "estimate.wdl:53:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/estimate.wdl/#L53"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fastqc.wdl"
message = "fastqc.wdl:10:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fastqc.wdl/#L10"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fastqc.wdl"
message = "fastqc.wdl:19:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fastqc.wdl/#L19"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fastqc.wdl"
message = "fastqc.wdl:23:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fastqc.wdl/#L23"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fastqc.wdl"
message = "fastqc.wdl:67:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fastqc.wdl/#L67"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:106:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L106"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:116:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L116"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:120:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L120"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:143:30: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L143"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:145:9: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L145"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:156:15: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L156"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:158:17: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L158"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:16:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L16"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:172:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L172"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:20:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L20"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:24:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L24"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:32:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L32"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:37:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L37"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:40:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L40"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:45:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L45"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:48:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L48"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:53:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L53"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/fq.wdl"
message = "fq.wdl:96:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/fq.wdl/#L96"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:12:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L12"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:150:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L150"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:161:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L161"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:162:10: note[BlankLinesBetweenElements]: extra blank line(s) found"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L162"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:214:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L214"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:225:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L225"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:234:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L234"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:244:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L244"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:300:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L300"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:311:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L311"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:324:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L324"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:328:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L328"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:373:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L373"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:385:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L385"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:397:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L397"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:400:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L400"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:409:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L409"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:417:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L417"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:423:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L423"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:486:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L486"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/gatk4.wdl"
message = "gatk4.wdl:69:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/gatk4.wdl/#L69"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:135:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L135"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:19:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L19"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:206:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L206"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:22:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L22"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:28:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L28"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:32:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L32"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:37:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L37"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:40:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L40"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:45:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L45"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:49:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L49"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:53:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L53"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:57:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L57"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:61:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L61"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/htseq.wdl"
message = "htseq.wdl:65:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/htseq.wdl/#L65"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:118:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L118"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:175:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L175"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:192:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L192"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:197:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L197"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:205:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L205"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:259:15: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L259"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:261:17: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L261"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:284:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L284"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:295:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L295"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:297:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L297"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:299:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L299"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:311:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L311"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:316:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L316"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:321:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L321"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:330:14: note[DisallowedInputName]: declaration identifier must be at least 3 characters"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L330"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:351:24: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L351"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:353:9: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L353"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:398:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L398"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:44:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L44"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:60:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L60"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:72:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L72"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:85:32: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L85"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:85:45: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L85"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:89:28: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L89"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:89:41: note[ExpressionSpacing]: multi-line if...then...else must have a preceding space"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L89"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:90:18: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L90"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:90:33: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L90"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:90:40: note[ExpressionSpacing]: multi-line if...then...else must have a preceding space"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L90"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:91:13: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L91"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:91:18: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L91"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:91:33: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L91"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:91:40: note[ExpressionSpacing]: multi-line if...then...else must have a preceding space"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L91"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/kraken2.wdl"
message = "kraken2.wdl:92:13: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/kraken2.wdl/#L92"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/librarian.wdl"
message = "librarian.wdl:20:5: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/librarian.wdl/#L20"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/librarian.wdl"
message = "librarian.wdl:52:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/librarian.wdl/#L52"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/md5sum.wdl"
message = "md5sum.wdl:39:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/md5sum.wdl/#L39"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/mosdepth.wdl"
message = "mosdepth.wdl:11:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/mosdepth.wdl/#L11"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/mosdepth.wdl"
message = "mosdepth.wdl:23:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/mosdepth.wdl/#L23"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/mosdepth.wdl"
message = "mosdepth.wdl:69:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/mosdepth.wdl/#L69"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/multiqc.wdl"
message = "multiqc.wdl:21:21: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/multiqc.wdl/#L21"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/multiqc.wdl"
message = "multiqc.wdl:68:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/multiqc.wdl/#L68"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:106:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L106"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:140:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L140"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:159:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L159"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:163:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L163"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:204:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L204"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:21:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L21"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:223:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L223"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:25:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L25"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:281:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L281"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:29:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L29"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:303:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L303"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:307:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L307"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:311:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L311"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:315:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L315"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:33:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L33"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:369:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L369"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:387:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L387"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:391:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L391"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:395:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L395"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:399:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L399"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:403:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L403"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:407:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L407"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:427:21: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L427"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:427:33: note[ExpressionSpacing]: multi-line if...then...else must have a preceding space"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L427"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:429:7: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L429"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:429:7: note[ExpressionSpacing]: multi-line if...then...else must have a preceding space"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L429"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:451:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L451"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/ngsderive.wdl"
message = "ngsderive.wdl:87:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/ngsderive.wdl/#L87"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:1037:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L1037"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:125:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L125"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:145:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L145"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:14:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L14"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:153:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L153"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:159:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L159"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:163:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L163"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:167:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L167"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:190:28: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L190"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:192:9: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L192"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:194:29: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L194"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:196:9: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L196"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:247:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L247"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:259:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L259"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:26:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L26"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:270:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L270"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:272:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L272"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:280:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L280"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:29:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L29"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:330:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L330"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:342:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L342"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:355:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L355"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:357:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L357"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:364:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L364"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:38:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L38"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:417:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L417"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:429:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L429"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:441:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L441"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:46:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L46"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:485:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L485"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:497:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L497"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:511:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L511"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:52:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L52"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:548:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L548"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:560:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L560"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:562:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L562"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:574:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L574"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:610:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L610"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:622:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L622"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:626:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L626"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:628:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L628"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:641:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L641"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:681:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L681"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:693:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L693"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:695:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L695"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:707:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L707"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:743:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L743"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:754:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L754"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:766:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L766"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:802:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L802"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:819:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L819"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:842:49: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L842"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:842:56: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L842"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:847:36: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L847"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:858:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L858"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:869:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L869"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:897:14: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L897"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:898:14: note[DisallowedOutputName]: declaration identifier starts with 'output'"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L898"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:904:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L904"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:915:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L915"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:923:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L923"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:926:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L926"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/picard.wdl"
message = "picard.wdl:976:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/picard.wdl/#L976"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/qualimap.wdl"
message = "qualimap.wdl:11:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/qualimap.wdl/#L11"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/qualimap.wdl"
message = "qualimap.wdl:157:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/qualimap.wdl/#L157"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/qualimap.wdl"
message = "qualimap.wdl:22:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/qualimap.wdl/#L22"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/qualimap.wdl"
message = "qualimap.wdl:26:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/qualimap.wdl/#L26"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/qualimap.wdl"
message = "qualimap.wdl:89:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/qualimap.wdl/#L89"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:117:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L117"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:135:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L135"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:172:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L172"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:17:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L17"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:183:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L183"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:192:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L192"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:21:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L21"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:228:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L228"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:246:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L246"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:250:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L250"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:285:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L285"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:57:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L57"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:75:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L75"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/sambamba.wdl"
message = "sambamba.wdl:79:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/sambamba.wdl/#L79"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:1003:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L1003"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:1054:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L1054"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:1158:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L1158"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:1176:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L1176"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:1188:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L1188"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:1202:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L1202"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:1208:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L1208"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:1278:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L1278"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:1324:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L1324"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:153:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L153"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:171:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L171"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:175:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L175"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:211:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L211"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:228:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L228"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:232:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L232"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:270:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L270"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:281:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L281"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:291:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L291"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:295:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L295"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:39:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L39"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:416:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L416"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:436:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L436"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:440:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L440"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:503:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L503"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:523:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L523"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:527:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L527"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:531:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L531"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:535:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L535"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:539:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L539"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:543:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L543"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:55:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L55"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:605:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L605"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:60:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L60"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:623:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L623"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:628:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L628"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:632:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L632"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:636:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L636"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:640:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L640"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:64:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L64"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:68:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L68"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:690:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L690"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:708:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L708"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:712:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L712"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:716:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L716"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:72:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L72"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:763:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L763"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:788:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L788"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:792:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L792"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:796:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L796"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:800:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L800"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:804:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L804"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:808:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L808"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:814:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L814"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:818:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L818"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:822:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L822"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:894:15: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L894"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:896:17: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L896"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:899:17: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L899"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:899:31: note[ExpressionSpacing]: multi-line if...then...else must have a preceding space"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L899"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:902:17: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L902"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:905:17: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L905"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:905:31: note[ExpressionSpacing]: multi-line if...then...else must have a preceding space"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L905"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:908:17: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L908"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:911:17: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L911"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:911:31: note[ExpressionSpacing]: multi-line if...then...else must have a preceding space"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L911"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:913:40: note[ExpressionSpacing]: operators must be surrounded by whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L913"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:916:17: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L916"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:919:17: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L919"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:921:17: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L921"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:956:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L956"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:973:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L973"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:980:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L980"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:982:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L982"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/samtools.wdl"
message = "samtools.wdl:999:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/samtools.wdl/#L999"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:130:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L130"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:154:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L154"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:167:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L167"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:169:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L169"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:174:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L174"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:176:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L176"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:185:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L185"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:188:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L188"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:18:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L18"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:195:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L195"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:197:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L197"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:213:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L213"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:215:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L215"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:219:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L219"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:221:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L221"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:226:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L226"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:228:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L228"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:22:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L22"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:233:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L233"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:235:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L235"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:240:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L240"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:242:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L242"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:249:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L249"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:251:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L251"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:258:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L258"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:260:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L260"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:266:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L266"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:268:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L268"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:274:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L274"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:276:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L276"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:280:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L280"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:284:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L284"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:291:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L291"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:293:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L293"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:299:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L299"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:301:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L301"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:308:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L308"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:311:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L311"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:315:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L315"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:317:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L317"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:31:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L31"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:324:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L324"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:326:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L326"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:332:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L332"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:334:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L334"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:338:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L338"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:350:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L350"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:354:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L354"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:358:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L358"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:372:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L372"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:376:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L376"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:380:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L380"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:384:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L384"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:39:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L39"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:405:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L405"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:409:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L409"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:413:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L413"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:417:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L417"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:421:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L421"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:435:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L435"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:439:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L439"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:43:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L43"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:443:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L443"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:449:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L449"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:453:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L453"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:457:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L457"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:461:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L461"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:467:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L467"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:471:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L471"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:487:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L487"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:493:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L493"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:499:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L499"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:505:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L505"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:511:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L511"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:654:17: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L654"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:656:17: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L656"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:678:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L678"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:684:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L684"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:690:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L690"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:696:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L696"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:702:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L702"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:726:17: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L726"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:728:17: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L728"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/star.wdl"
message = "star.wdl:823:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/star.wdl/#L823"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:101:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L101"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:120:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L120"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:125:16: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L125"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:142:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L142"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:161:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L161"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:242:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L242"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:279:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L279"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:324:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L324"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:366:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L366"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:384:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L384"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:392:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L392"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:425:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L425"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:45:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L45"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:61:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L61"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:65:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L65"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:686:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L686"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:764:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L764"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:780:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L780"

[[diagnostics]]
document = "stjudecloud/workflows:/tools/util.wdl"
message = "util.wdl:825:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/tools/util.wdl/#L825"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/chipseq/chipseq-standard.wdl"
message = "chipseq-standard.wdl:10:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/chipseq/chipseq-standard.wdl/#L10"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/chipseq/chipseq-standard.wdl"
message = "chipseq-standard.wdl:11:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/chipseq/chipseq-standard.wdl/#L11"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/chipseq/chipseq-standard.wdl"
message = "chipseq-standard.wdl:124:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/chipseq/chipseq-standard.wdl/#L124"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/chipseq/chipseq-standard.wdl"
message = "chipseq-standard.wdl:12:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/chipseq/chipseq-standard.wdl/#L12"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/chipseq/chipseq-standard.wdl"
message = "chipseq-standard.wdl:21:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/chipseq/chipseq-standard.wdl/#L21"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/chipseq/chipseq-standard.wdl"
message = "chipseq-standard.wdl:89:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/chipseq/chipseq-standard.wdl/#L89"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/chipseq/chipseq-standard.wdl"
message = "chipseq-standard.wdl:95:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/chipseq/chipseq-standard.wdl/#L95"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl"
message = "dnaseq-core.wdl:17:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-core.wdl/#L17"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl"
message = "dnaseq-core.wdl:21:5: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-core.wdl/#L21"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl"
message = "dnaseq-core.wdl:30:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-core.wdl/#L30"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl"
message = "dnaseq-core.wdl:30:22: note[KeyValuePairs]: all items in an array or object should be on separate lines"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-core.wdl/#L30"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl"
message = "dnaseq-core.wdl:35:5: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-core.wdl/#L35"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl"
message = "dnaseq-core.wdl:67:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-core.wdl/#L67"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl"
message = "dnaseq-core.wdl:79:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-core.wdl/#L79"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl"
message = "dnaseq-core.wdl:84:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-core.wdl/#L84"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard-fastq.wdl"
message = "dnaseq-standard-fastq.wdl:116:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L116"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard-fastq.wdl"
message = "dnaseq-standard-fastq.wdl:116:22: note[KeyValuePairs]: all items in an array or object should be on separate lines"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L116"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard-fastq.wdl"
message = "dnaseq-standard-fastq.wdl:14:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L14"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard-fastq.wdl"
message = "dnaseq-standard-fastq.wdl:151:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L151"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard-fastq.wdl"
message = "dnaseq-standard-fastq.wdl:18:5: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L18"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard-fastq.wdl"
message = "dnaseq-standard-fastq.wdl:30:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L30"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard-fastq.wdl"
message = "dnaseq-standard-fastq.wdl:30:22: note[KeyValuePairs]: all items in an array or object should be on separate lines"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L30"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard-fastq.wdl"
message = "dnaseq-standard-fastq.wdl:36:5: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L36"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard-fastq.wdl"
message = "dnaseq-standard-fastq.wdl:51:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L51"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard-fastq.wdl"
message = "dnaseq-standard-fastq.wdl:54:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L54"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard-fastq.wdl"
message = "dnaseq-standard-fastq.wdl:79:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L79"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard-fastq.wdl"
message = "dnaseq-standard-fastq.wdl:84:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L84"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard-fastq.wdl"
message = "dnaseq-standard-fastq.wdl:96:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L96"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard.wdl"
message = "dnaseq-standard.wdl:104:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard.wdl/#L104"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard.wdl"
message = "dnaseq-standard.wdl:104:22: note[KeyValuePairs]: all items in an array or object should be on separate lines"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard.wdl/#L104"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard.wdl"
message = "dnaseq-standard.wdl:129:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard.wdl/#L129"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard.wdl"
message = "dnaseq-standard.wdl:16:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard.wdl/#L16"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard.wdl"
message = "dnaseq-standard.wdl:20:5: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard.wdl/#L20"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard.wdl"
message = "dnaseq-standard.wdl:27:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard.wdl/#L27"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard.wdl"
message = "dnaseq-standard.wdl:27:22: note[KeyValuePairs]: all items in an array or object should be on separate lines"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard.wdl/#L27"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-standard.wdl"
message = "dnaseq-standard.wdl:34:5: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/dnaseq/dnaseq-standard.wdl/#L34"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/general/alignment-post.wdl"
message = "alignment-post.wdl:15:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/general/alignment-post.wdl/#L15"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/general/alignment-post.wdl"
message = "alignment-post.wdl:26:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/general/alignment-post.wdl/#L26"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/general/alignment-post.wdl"
message = "alignment-post.wdl:29:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/general/alignment-post.wdl/#L29"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/general/alignment-post.wdl"
message = "alignment-post.wdl:58:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/general/alignment-post.wdl/#L58"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/general/alignment-post.wdl"
message = "alignment-post.wdl:6:1: note[LineWidth]: line exceeds maximum width of 90"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/general/alignment-post.wdl/#L6"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/general/alignment-post.wdl"
message = "alignment-post.wdl:70:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/general/alignment-post.wdl/#L70"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/general/bam-to-fastqs.wdl"
message = "bam-to-fastqs.wdl:11:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/general/bam-to-fastqs.wdl/#L11"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/general/samtools-merge.wdl"
message = "samtools-merge.wdl:15:5: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/general/samtools-merge.wdl/#L15"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/general/samtools-merge.wdl"
message = "samtools-merge.wdl:21:5: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/general/samtools-merge.wdl/#L21"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/markdups-post.wdl"
message = "markdups-post.wdl:25:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/markdups-post.wdl/#L25"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:181:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L181"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:185:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L185"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:187:36: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L187"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:189:9: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L189"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:34:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L34"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:39:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L39"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:451:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L451"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:463:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L463"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:467:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L467"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:47:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L47"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:556:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L556"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:57:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L57"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:67:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L67"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/qc/quality-check-standard.wdl"
message = "quality-check-standard.wdl:74:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/qc/quality-check-standard.wdl/#L74"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/reference/bwa-db-build.wdl"
message = "bwa-db-build.wdl:11:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/reference/bwa-db-build.wdl/#L11"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl"
message = "gatk-reference.wdl:17:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/reference/gatk-reference.wdl/#L17"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl"
message = "gatk-reference.wdl:57:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/reference/gatk-reference.wdl/#L57"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl"
message = "gatk-reference.wdl:70:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/reference/gatk-reference.wdl/#L70"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl"
message = "gatk-reference.wdl:76:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/reference/gatk-reference.wdl/#L76"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl"
message = "gatk-reference.wdl:83:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/reference/gatk-reference.wdl/#L83"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl"
message = "gatk-reference.wdl:90:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/reference/gatk-reference.wdl/#L90"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/reference/make-qc-reference.wdl"
message = "make-qc-reference.wdl:137:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/reference/make-qc-reference.wdl/#L137"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/reference/make-qc-reference.wdl"
message = "make-qc-reference.wdl:23:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/reference/make-qc-reference.wdl/#L23"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/reference/make-qc-reference.wdl"
message = "make-qc-reference.wdl:34:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/reference/make-qc-reference.wdl/#L34"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/reference/make-qc-reference.wdl"
message = "make-qc-reference.wdl:40:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/reference/make-qc-reference.wdl/#L40"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/reference/make-qc-reference.wdl"
message = "make-qc-reference.wdl:48:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/reference/make-qc-reference.wdl/#L48"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/reference/star-db-build.wdl"
message = "star-db-build.wdl:12:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/reference/star-db-build.wdl/#L12"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/ESTIMATE.wdl"
message = "ESTIMATE.wdl:12:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/ESTIMATE.wdl/#L12"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:105:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L105"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:111:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L111"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:127:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L127"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:151:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L151"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:196:33: note[ExpressionSpacing]: multi-line if...then...else must have a preceding parenthesis and newline"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L196"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:198:9: note[ExpressionSpacing]: multi-line if...then...else must have a following newline and parenthesis"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L198"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:20:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L20"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:36:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L36"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:40:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L40"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:45:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L45"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:48:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L48"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:53:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L53"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:57:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L57"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:66:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L66"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:72:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L72"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:77:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L77"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:82:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L82"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:87:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L87"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:93:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L93"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl"
message = "rnaseq-core.wdl:99:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-core.wdl/#L99"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard-fastq.wdl"
message = "rnaseq-standard-fastq.wdl:112:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L112"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard-fastq.wdl"
message = "rnaseq-standard-fastq.wdl:143:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L143"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard-fastq.wdl"
message = "rnaseq-standard-fastq.wdl:148:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L148"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard-fastq.wdl"
message = "rnaseq-standard-fastq.wdl:36:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L36"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard-fastq.wdl"
message = "rnaseq-standard-fastq.wdl:49:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L49"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard-fastq.wdl"
message = "rnaseq-standard-fastq.wdl:63:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L63"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard-fastq.wdl"
message = "rnaseq-standard-fastq.wdl:70:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L70"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard-fastq.wdl"
message = "rnaseq-standard-fastq.wdl:73:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L73"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard-fastq.wdl"
message = "rnaseq-standard-fastq.wdl:78:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L78"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard-fastq.wdl"
message = "rnaseq-standard-fastq.wdl:82:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L82"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard.wdl"
message = "rnaseq-standard.wdl:141:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard.wdl/#L141"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard.wdl"
message = "rnaseq-standard.wdl:145:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard.wdl/#L145"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard.wdl"
message = "rnaseq-standard.wdl:153:16: note[DisallowedInputName]: declaration identifier starts with 'input'"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard.wdl/#L153"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard.wdl"
message = "rnaseq-standard.wdl:182:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard.wdl/#L182"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard.wdl"
message = "rnaseq-standard.wdl:20:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard.wdl/#L20"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard.wdl"
message = "rnaseq-standard.wdl:33:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard.wdl/#L33"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard.wdl"
message = "rnaseq-standard.wdl:36:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard.wdl/#L36"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard.wdl"
message = "rnaseq-standard.wdl:41:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard.wdl/#L41"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard.wdl"
message = "rnaseq-standard.wdl:45:17: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard.wdl/#L45"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-standard.wdl"
message = "rnaseq-standard.wdl:73:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-standard.wdl/#L73"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl"
message = "rnaseq-variant-calling.wdl:106:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-variant-calling.wdl/#L106"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl"
message = "rnaseq-variant-calling.wdl:115:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-variant-calling.wdl/#L115"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl"
message = "rnaseq-variant-calling.wdl:13:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-variant-calling.wdl/#L13"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl"
message = "rnaseq-variant-calling.wdl:51:9: note[ExpressionSpacing]: prefix operators may not contain whitespace"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-variant-calling.wdl/#L51"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl"
message = "rnaseq-variant-calling.wdl:54:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-variant-calling.wdl/#L54"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl"
message = "rnaseq-variant-calling.wdl:75:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-variant-calling.wdl/#L75"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl"
message = "rnaseq-variant-calling.wdl:82:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-variant-calling.wdl/#L82"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl"
message = "rnaseq-variant-calling.wdl:87:9: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-variant-calling.wdl/#L87"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl"
message = "rnaseq-variant-calling.wdl:99:13: note[TrailingComma]: item missing trailing comma"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/rnaseq/rnaseq-variant-calling.wdl/#L99"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
message = "10x-bam-to-fastqs.wdl:18:5: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L18"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
message = "10x-bam-to-fastqs.wdl:64:5: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L64"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
message = "10x-bam-to-fastqs.wdl:69:5: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L69"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/scrnaseq/10x-bam-to-fastqs.wdl"
message = "10x-bam-to-fastqs.wdl:93:20: note[ContainerValue]: container URI uses a mutable tag"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L93"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/scrnaseq/scrnaseq-standard.wdl"
message = "scrnaseq-standard.wdl:32:5: note[BlankLinesBetweenElements]: missing blank line"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/scrnaseq/scrnaseq-standard.wdl/#L32"

[[diagnostics]]
document = "stjudecloud/workflows:/workflows/scrnaseq/scrnaseq-standard.wdl"
message = "scrnaseq-standard.wdl:91:14: note[DisallowedOutputName]: declaration identifier must be at least 3 characters"
permalink = "https://github.com/stjudecloud/workflows/blob/a56ad9b8c7de5c9b13350f465c1543d0cb0b6b1a/workflows/scrnaseq/scrnaseq-standard.wdl/#L91"