From 48ad131fc36741f45364c5119e5570d3b6f2b103 Mon Sep 17 00:00:00 2001 From: Peter Huene Date: Fri, 27 Sep 2024 18:57:02 -0700 Subject: [PATCH] chore: update gauntlet. --- Arena.toml | 1158 ++++++++++++++++++++++++------------------------- Gauntlet.toml | 93 ++-- 2 files changed, 628 insertions(+), 623 deletions(-) diff --git a/Arena.toml b/Arena.toml index 3c64d9ad..24de21dc 100644 --- a/Arena.toml +++ b/Arena.toml @@ -12,7 +12,7 @@ commit_hash = "c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2" [repositories."stjudecloud/workflows"] identifier = "stjudecloud/workflows" -commit_hash = "129060215443bbd1b67c4d3d149d48acdab90ef2" +commit_hash = "8a709b25b8a0d0b850c4adb1ba915293d9d024d1" filters = ["/template/task-templates.wdl"] [[diagnostics]] @@ -1738,2889 +1738,2889 @@ permalink = "https://github.com/getwilds/ww-vc-trio/blob/c2c13e85efda8ac7aca7f87 [[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/129060215443bbd1b67c4d3d149d48acdab90ef2/data_structures/flag_filter.wdl/#L119" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/data_structures/flag_filter.wdl/#L119" [[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/129060215443bbd1b67c4d3d149d48acdab90ef2/data_structures/read_group.wdl/#L107" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/data_structures/read_group.wdl/#L159" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/data_structures/read_group.wdl/#L192" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/data_structures/read_group.wdl/#L444" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L102" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L11" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L142" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L22" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L245" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L26" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L298" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L308" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L30" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L347" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L34" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L38" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L397" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L44" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L80" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L87" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L93" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/arriba.wdl/#L97" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L105" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L109" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L115" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L119" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L123" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L171" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L171" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L190" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L19" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L210" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L214" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L218" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L23" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L264" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L264" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L268" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L268" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L27" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L286" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L303" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L337" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/bwa.wdl/#L89" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/cellranger.wdl/#L113" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/cellranger.wdl/#L154" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/cellranger.wdl/#L154" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/cellranger.wdl/#L155" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/cellranger.wdl/#L155" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/cellranger.wdl/#L155" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/cellranger.wdl/#L156" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/cellranger.wdl/#L156" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/cellranger.wdl/#L156" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/cellranger.wdl/#L157" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/cellranger.wdl/#L184" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/cellranger.wdl/#L43" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/cellranger.wdl/#L43" [[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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/cellranger.wdl/#L95" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/deeptools.wdl/#L19" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/deeptools.wdl/#L23" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/deeptools.wdl/#L70" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/estimate.wdl/#L39" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/estimate.wdl/#L53" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fastqc.wdl/#L10" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fastqc.wdl/#L19" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fastqc.wdl/#L23" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fastqc.wdl/#L67" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L106" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L116" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L120" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L143" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L145" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L156" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L158" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L16" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L172" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L20" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L24" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L32" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L37" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L40" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L45" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L48" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L53" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/fq.wdl/#L96" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L12" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L12" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:152:20: note[ContainerValue]: container URI uses a mutable tag" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L152" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L152" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:163:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L163" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L163" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:164:10: note[BlankLinesBetweenElements]: extra blank line(s) found" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L164" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L164" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:216:20: note[ContainerValue]: container URI uses a mutable tag" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L216" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L216" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:227:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L227" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L227" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:236:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L236" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L236" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:246:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L246" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L246" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:302:20: note[ContainerValue]: container URI uses a mutable tag" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L302" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L302" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:313:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L313" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L313" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:326:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L326" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L326" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:330:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L330" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L330" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:375:20: note[ContainerValue]: container URI uses a mutable tag" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L375" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L375" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:387:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L387" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L387" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:399:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L399" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L399" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:402:17: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L402" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L402" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:411:17: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L411" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L411" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:419:17: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L419" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L419" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:425:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L425" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L425" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:488:20: note[ContainerValue]: container URI uses a mutable tag" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L488" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L488" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" message = "gatk4.wdl:71:20: note[ContainerValue]: container URI uses a mutable tag" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/gatk4.wdl/#L71" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/tools/gatk4.wdl/#L71" [[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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L135" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L19" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L206" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L22" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L28" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L32" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L37" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L40" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L45" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L49" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L53" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L57" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L61" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/htseq.wdl/#L65" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L118" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L175" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L192" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L197" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L205" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L259" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L261" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L284" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L295" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L297" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L299" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L311" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L316" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L321" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L330" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L351" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L353" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L398" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L44" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L60" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L72" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L85" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L85" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L89" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L89" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L90" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L90" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L90" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L91" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L91" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L91" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L91" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/kraken2.wdl/#L92" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/librarian.wdl/#L20" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/librarian.wdl/#L52" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/md5sum.wdl/#L39" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/mosdepth.wdl/#L11" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/mosdepth.wdl/#L23" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/mosdepth.wdl/#L69" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/multiqc.wdl/#L21" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/multiqc.wdl/#L68" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L106" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L140" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L159" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L163" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L204" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L21" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L223" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L25" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L281" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L29" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L303" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L307" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L311" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L315" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L33" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L369" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L387" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L391" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L395" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L399" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L403" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L407" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L427" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L427" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L429" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L429" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L451" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/ngsderive.wdl/#L87" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L1037" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L125" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L145" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L14" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L153" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L159" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L163" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L167" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L190" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L192" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L194" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L196" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L247" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L259" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L26" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L270" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L272" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L280" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L29" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L330" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L342" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L355" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L357" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L364" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L38" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L417" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L429" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L441" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L46" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L485" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L497" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L511" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L52" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L548" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L560" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L562" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L574" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L610" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L622" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L626" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L628" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L641" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L681" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L693" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L695" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L707" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L743" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L754" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L766" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L802" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L819" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L842" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L842" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L847" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L858" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L869" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L897" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L898" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L904" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L915" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L923" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L926" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/picard.wdl/#L976" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/qualimap.wdl/#L11" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/qualimap.wdl/#L157" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/qualimap.wdl/#L22" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/qualimap.wdl/#L26" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/qualimap.wdl/#L89" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L117" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L135" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L172" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L17" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L183" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L192" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L21" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L228" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L246" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L250" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L285" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L57" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L75" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/sambamba.wdl/#L79" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L1003" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L1054" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L1158" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L1176" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L1188" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L1202" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L1208" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L1278" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L1324" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L153" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L171" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L175" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L211" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L228" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L232" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L270" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L281" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L291" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L295" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L39" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L416" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L436" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L440" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L503" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L523" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L527" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L531" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L535" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L539" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L543" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L55" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L605" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L60" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L623" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L628" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L632" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L636" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L640" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L64" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L68" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L690" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L708" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L712" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L716" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L72" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L763" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L788" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L792" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L796" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L800" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L804" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L808" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L814" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L818" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L822" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L894" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L896" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L899" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L899" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L902" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L905" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L905" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L908" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L911" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L911" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L913" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L916" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L919" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L921" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L956" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L973" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L980" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L982" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/samtools.wdl/#L999" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L130" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L154" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L167" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L169" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L174" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L176" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L185" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L188" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L18" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L195" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L197" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L213" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L215" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L219" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L221" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L226" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L228" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L22" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L233" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L235" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L240" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L242" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L249" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L251" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L258" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L260" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L266" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L268" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L274" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L276" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L280" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L284" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L291" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L293" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L299" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L301" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L308" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L311" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L315" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L317" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L31" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L324" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L326" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L332" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L334" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L338" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L350" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L354" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L358" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L372" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L376" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L380" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L384" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L39" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L405" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L409" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L413" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L417" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L421" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L435" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L439" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L43" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L443" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L449" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L453" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L457" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L461" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L467" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L471" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L487" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L493" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L499" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L505" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L511" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L654" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L656" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L678" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L684" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L690" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L696" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L702" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L726" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L728" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/star.wdl/#L823" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L101" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L120" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L125" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L142" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L161" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L242" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L279" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L324" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L366" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L384" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L392" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L425" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L45" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L61" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L65" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L686" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L764" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L780" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/tools/util.wdl/#L825" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/chipseq/chipseq-standard.wdl/#L10" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/chipseq/chipseq-standard.wdl/#L11" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/chipseq/chipseq-standard.wdl/#L124" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/chipseq/chipseq-standard.wdl/#L12" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/chipseq/chipseq-standard.wdl/#L21" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/chipseq/chipseq-standard.wdl/#L89" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/chipseq/chipseq-standard.wdl/#L95" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/chipseq/chipseq-standard.wdl/#L95" [[diagnostics]] document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl" message = "dnaseq-core.wdl:18:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-core.wdl/#L18" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/dnaseq/dnaseq-core.wdl/#L18" [[diagnostics]] document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl" message = "dnaseq-core.wdl:22:5: note[BlankLinesBetweenElements]: missing blank line" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-core.wdl/#L22" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/dnaseq/dnaseq-core.wdl/#L22" [[diagnostics]] document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl" message = "dnaseq-core.wdl:31:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-core.wdl/#L31" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/dnaseq/dnaseq-core.wdl/#L31" [[diagnostics]] document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl" message = "dnaseq-core.wdl:31:22: note[KeyValuePairs]: all items in an array or object should be on separate lines" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-core.wdl/#L31" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/dnaseq/dnaseq-core.wdl/#L31" [[diagnostics]] document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl" message = "dnaseq-core.wdl:36:5: note[BlankLinesBetweenElements]: missing blank line" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-core.wdl/#L36" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/dnaseq/dnaseq-core.wdl/#L36" [[diagnostics]] document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl" message = "dnaseq-core.wdl:68:17: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-core.wdl/#L68" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/dnaseq/dnaseq-core.wdl/#L68" [[diagnostics]] document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl" message = "dnaseq-core.wdl:80:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-core.wdl/#L80" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/dnaseq/dnaseq-core.wdl/#L80" [[diagnostics]] document = "stjudecloud/workflows:/workflows/dnaseq/dnaseq-core.wdl" message = "dnaseq-core.wdl:85:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-core.wdl/#L85" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/dnaseq/dnaseq-core.wdl/#L85" [[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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L116" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L116" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L14" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L151" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L18" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L30" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L30" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L36" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L51" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L54" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L79" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L84" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard-fastq.wdl/#L96" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard.wdl/#L104" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard.wdl/#L104" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard.wdl/#L129" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard.wdl/#L16" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard.wdl/#L20" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard.wdl/#L27" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard.wdl/#L27" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/dnaseq/dnaseq-standard.wdl/#L34" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/general/alignment-post.wdl/#L15" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/general/alignment-post.wdl/#L26" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/general/alignment-post.wdl/#L29" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/general/alignment-post.wdl/#L58" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/general/alignment-post.wdl/#L6" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/general/alignment-post.wdl/#L70" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/general/bam-to-fastqs.wdl/#L11" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/general/samtools-merge.wdl/#L15" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/general/samtools-merge.wdl/#L21" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/markdups-post.wdl/#L25" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L181" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L185" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L187" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L189" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L34" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L39" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L451" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L463" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L467" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L47" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L556" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L57" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L67" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/qc/quality-check-standard.wdl/#L74" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/reference/bwa-db-build.wdl/#L11" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/reference/gatk-reference.wdl/#L17" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/reference/gatk-reference.wdl/#L57" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/reference/gatk-reference.wdl/#L70" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/reference/gatk-reference.wdl/#L76" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/reference/gatk-reference.wdl/#L83" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/reference/gatk-reference.wdl/#L90" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/reference/make-qc-reference.wdl/#L137" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/reference/make-qc-reference.wdl/#L23" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/reference/make-qc-reference.wdl/#L34" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/reference/make-qc-reference.wdl/#L40" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/reference/make-qc-reference.wdl/#L48" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/reference/star-db-build.wdl/#L12" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/ESTIMATE.wdl/#L12" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L105" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L111" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L127" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L151" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L196" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L198" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L20" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L36" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L40" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L45" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L48" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L53" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L57" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L66" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L72" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L77" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L82" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L87" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L93" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-core.wdl/#L99" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L112" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L143" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L148" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L36" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L49" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L63" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L70" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L73" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L78" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard-fastq.wdl/#L82" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard.wdl/#L141" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard.wdl/#L145" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard.wdl/#L153" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard.wdl/#L182" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard.wdl/#L20" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard.wdl/#L33" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard.wdl/#L36" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard.wdl/#L41" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard.wdl/#L45" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-standard.wdl/#L73" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/rnaseq/rnaseq-standard.wdl/#L73" [[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl" message = "rnaseq-variant-calling.wdl:100:13: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-variant-calling.wdl/#L100" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/rnaseq/rnaseq-variant-calling.wdl/#L100" [[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl" message = "rnaseq-variant-calling.wdl:107:9: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-variant-calling.wdl/#L107" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/rnaseq/rnaseq-variant-calling.wdl/#L107" [[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl" message = "rnaseq-variant-calling.wdl:116:9: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-variant-calling.wdl/#L116" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/rnaseq/rnaseq-variant-calling.wdl/#L116" [[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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-variant-calling.wdl/#L13" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-variant-calling.wdl/#L51" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-variant-calling.wdl/#L54" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/rnaseq/rnaseq-variant-calling.wdl/#L54" [[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl" message = "rnaseq-variant-calling.wdl:64:9: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-variant-calling.wdl/#L64" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/rnaseq/rnaseq-variant-calling.wdl/#L64" [[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl" message = "rnaseq-variant-calling.wdl:76:9: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-variant-calling.wdl/#L76" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/rnaseq/rnaseq-variant-calling.wdl/#L76" [[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl" message = "rnaseq-variant-calling.wdl:83:9: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-variant-calling.wdl/#L83" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/rnaseq/rnaseq-variant-calling.wdl/#L83" [[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl" message = "rnaseq-variant-calling.wdl:88:9: note[TrailingComma]: item missing trailing comma" -permalink = "https://github.com/stjudecloud/workflows/blob/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/rnaseq/rnaseq-variant-calling.wdl/#L88" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/rnaseq/rnaseq-variant-calling.wdl/#L88" [[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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L18" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L64" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L69" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/scrnaseq/10x-bam-to-fastqs.wdl/#L93" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/scrnaseq/scrnaseq-standard.wdl/#L32" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/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/129060215443bbd1b67c4d3d149d48acdab90ef2/workflows/scrnaseq/scrnaseq-standard.wdl/#L91" +permalink = "https://github.com/stjudecloud/workflows/blob/8a709b25b8a0d0b850c4adb1ba915293d9d024d1/workflows/scrnaseq/scrnaseq-standard.wdl/#L91" diff --git a/Gauntlet.toml b/Gauntlet.toml index 3c013288..64e4f550 100644 --- a/Gauntlet.toml +++ b/Gauntlet.toml @@ -4,7 +4,7 @@ commit_hash = "26eeda81a0540dc793fc69b0c390d232ca7ca50a" [repositories."PacificBiosciences/HiFi-human-WGS-WDL"] identifier = "PacificBiosciences/HiFi-human-WGS-WDL" -commit_hash = "9a1a2846443e4b621f1dca0259fd3fa21885156a" +commit_hash = "1cf2b2e80024290d0ec1ea93b6a279ea2de519b0" [repositories."aws-samples/amazon-omics-tutorials"] identifier = "aws-samples/amazon-omics-tutorials" @@ -20,11 +20,11 @@ commit_hash = "4536dd2c6719b86f4c50348f0ce354818260cadb" [repositories."broadinstitute/palantir-workflows"] identifier = "broadinstitute/palantir-workflows" -commit_hash = "ae5b3026ea0102ab4164d30d552cabfc16076b44" +commit_hash = "84111f54323074954fd18b2723a111e533726d8f" [repositories."broadinstitute/warp"] identifier = "broadinstitute/warp" -commit_hash = "9b5e498e19b89ef72a2c27bb68884c54de768d76" +commit_hash = "0c6697b5b017be4f0335077f7807b67c091fdbac" [repositories."chanzuckerberg/czid-workflows"] identifier = "chanzuckerberg/czid-workflows" @@ -44,12 +44,12 @@ commit_hash = "c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2" [repositories."stjudecloud/workflows"] identifier = "stjudecloud/workflows" -commit_hash = "129060215443bbd1b67c4d3d149d48acdab90ef2" +commit_hash = "8a709b25b8a0d0b850c4adb1ba915293d9d024d1" filters = ["/template/task-templates.wdl"] [repositories."theiagen/public_health_bioinformatics"] identifier = "theiagen/public_health_bioinformatics" -commit_hash = "109e5878fd71d4102dff91110d18d6d6f1d2c002" +commit_hash = "8c91ecdec2ca3a1c85adc9e182caa126b6437024" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl" @@ -379,152 +379,157 @@ permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026 [[diagnostics]] document = "broadinstitute/palantir-workflows:/BenchmarkSVs/BenchmarkSVs.wdl" message = "BenchmarkSVs.wdl:457:40: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/BenchmarkSVs/BenchmarkSVs.wdl/#L457" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/BenchmarkSVs/BenchmarkSVs.wdl/#L457" [[diagnostics]] document = "broadinstitute/palantir-workflows:/BenchmarkSVs/BenchmarkSVs.wdl" message = "BenchmarkSVs.wdl:485:43: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/BenchmarkSVs/BenchmarkSVs.wdl/#L485" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/BenchmarkSVs/BenchmarkSVs.wdl/#L485" [[diagnostics]] document = "broadinstitute/palantir-workflows:/BenchmarkSVs/BenchmarkSVs.wdl" message = "BenchmarkSVs.wdl:772:43: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/BenchmarkSVs/BenchmarkSVs.wdl/#L772" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/BenchmarkSVs/BenchmarkSVs.wdl/#L772" [[diagnostics]] document = "broadinstitute/palantir-workflows:/BenchmarkSVs/BenchmarkSVs.wdl" message = "BenchmarkSVs.wdl:789:36: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/BenchmarkSVs/BenchmarkSVs.wdl/#L789" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/BenchmarkSVs/BenchmarkSVs.wdl/#L789" [[diagnostics]] document = "broadinstitute/palantir-workflows:/BenchmarkSVs/BenchmarkSVs.wdl" message = "BenchmarkSVs.wdl:790:42: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/BenchmarkSVs/BenchmarkSVs.wdl/#L790" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/BenchmarkSVs/BenchmarkSVs.wdl/#L790" [[diagnostics]] document = "broadinstitute/palantir-workflows:/BenchmarkSVs/BenchmarkSVs.wdl" message = "BenchmarkSVs.wdl:890:36: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/BenchmarkSVs/BenchmarkSVs.wdl/#L890" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/BenchmarkSVs/BenchmarkSVs.wdl/#L890" [[diagnostics]] -document = "broadinstitute/palantir-workflows:/BenchmarkVCFs/SimpleBenchmark.wdl" -message = "SimpleBenchmark.wdl:551:36: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/BenchmarkVCFs/SimpleBenchmark.wdl/#L551" +document = "broadinstitute/palantir-workflows:/BenchmarkVCFs/BenchmarkVCFs.wdl" +message = "BenchmarkVCFs.wdl:613:36: error: a placeholder cannot have more than one option" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/BenchmarkVCFs/BenchmarkVCFs.wdl/#L613" [[diagnostics]] -document = "broadinstitute/palantir-workflows:/BenchmarkVCFs/SimpleBenchmark.wdl" -message = "SimpleBenchmark.wdl:565:36: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/BenchmarkVCFs/SimpleBenchmark.wdl/#L565" +document = "broadinstitute/palantir-workflows:/BenchmarkVCFs/BenchmarkVCFs.wdl" +message = "BenchmarkVCFs.wdl:621:36: error: a placeholder cannot have more than one option" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/BenchmarkVCFs/BenchmarkVCFs.wdl/#L621" [[diagnostics]] -document = "broadinstitute/palantir-workflows:/BenchmarkVCFs/SimpleBenchmark.wdl" -message = "SimpleBenchmark.wdl:570:36: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/BenchmarkVCFs/SimpleBenchmark.wdl/#L570" +document = "broadinstitute/palantir-workflows:/BenchmarkVCFs/BenchmarkVCFs.wdl" +message = "BenchmarkVCFs.wdl:626:36: error: a placeholder cannot have more than one option" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/BenchmarkVCFs/BenchmarkVCFs.wdl/#L626" [[diagnostics]] -document = "broadinstitute/palantir-workflows:/BenchmarkVCFs/SimpleBenchmark.wdl" -message = "SimpleBenchmark.wdl:575:36: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/BenchmarkVCFs/SimpleBenchmark.wdl/#L575" +document = "broadinstitute/palantir-workflows:/BenchmarkVCFs/BenchmarkVCFs.wdl" +message = "BenchmarkVCFs.wdl:631:36: error: a placeholder cannot have more than one option" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/BenchmarkVCFs/BenchmarkVCFs.wdl/#L631" [[diagnostics]] document = "broadinstitute/palantir-workflows:/HaplotypeMap/BuildHaplotypeMap.wdl" message = "BuildHaplotypeMap.wdl:17:1: error: a WDL document must start with a version statement" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/HaplotypeMap/BuildHaplotypeMap.wdl/#L17" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/HaplotypeMap/BuildHaplotypeMap.wdl/#L17" [[diagnostics]] document = "broadinstitute/palantir-workflows:/Utilities/IntervalFiles/ComputeIntervalBamStats.wdl" message = "ComputeIntervalBamStats.wdl:223:37: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/Utilities/IntervalFiles/ComputeIntervalBamStats.wdl/#L223" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/Utilities/IntervalFiles/ComputeIntervalBamStats.wdl/#L223" [[diagnostics]] document = "broadinstitute/palantir-workflows:/Utilities/IntervalFiles/ComputeIntervalBamStats.wdl" message = "ComputeIntervalBamStats.wdl:270:37: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/Utilities/IntervalFiles/ComputeIntervalBamStats.wdl/#L270" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/Utilities/IntervalFiles/ComputeIntervalBamStats.wdl/#L270" [[diagnostics]] document = "broadinstitute/palantir-workflows:/Utilities/WDLs/CreateIGVSession.wdl" message = "CreateIGVSession.wdl:51:36: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/Utilities/WDLs/CreateIGVSession.wdl/#L51" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/Utilities/WDLs/CreateIGVSession.wdl/#L51" [[diagnostics]] document = "broadinstitute/palantir-workflows:/Utilities/WDLs/CreateIGVSession.wdl" message = "CreateIGVSession.wdl:52:36: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/Utilities/WDLs/CreateIGVSession.wdl/#L52" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/Utilities/WDLs/CreateIGVSession.wdl/#L52" [[diagnostics]] document = "broadinstitute/palantir-workflows:/Utilities/WDLs/CreateIGVSession.wdl" message = "CreateIGVSession.wdl:53:46: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/palantir-workflows/blob/ae5b3026ea0102ab4164d30d552cabfc16076b44/Utilities/WDLs/CreateIGVSession.wdl/#L53" +permalink = "https://github.com/broadinstitute/palantir-workflows/blob/84111f54323074954fd18b2723a111e533726d8f/Utilities/WDLs/CreateIGVSession.wdl/#L53" + +[[diagnostics]] +document = "broadinstitute/warp:/pipelines/skylab/multiome/Multiome.wdl" +message = "Multiome.wdl:104:13: error: duplicate call input `cloud_provider` in call statement" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/pipelines/skylab/multiome/Multiome.wdl/#L104" [[diagnostics]] document = "broadinstitute/warp:/pipelines/skylab/scATAC/scATAC.wdl" message = "scATAC.wdl:203:9: error: duplicate key `cpu` in runtime section" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/pipelines/skylab/scATAC/scATAC.wdl/#L203" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/pipelines/skylab/scATAC/scATAC.wdl/#L203" [[diagnostics]] document = "broadinstitute/warp:/tasks/broad/Funcotator.wdl" message = "Funcotator.wdl:163:92: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/tasks/broad/Funcotator.wdl/#L163" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/tasks/broad/Funcotator.wdl/#L163" [[diagnostics]] document = "broadinstitute/warp:/tasks/broad/Funcotator.wdl" message = "Funcotator.wdl:164:89: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/tasks/broad/Funcotator.wdl/#L164" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/tasks/broad/Funcotator.wdl/#L164" [[diagnostics]] document = "broadinstitute/warp:/tasks/broad/Funcotator.wdl" message = "Funcotator.wdl:165:91: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/tasks/broad/Funcotator.wdl/#L165" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/tasks/broad/Funcotator.wdl/#L165" [[diagnostics]] document = "broadinstitute/warp:/tasks/broad/GermlineVariantDiscovery.wdl" message = "GermlineVariantDiscovery.wdl:140:32: error: expected string, but found integer" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/tasks/broad/GermlineVariantDiscovery.wdl/#L140" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/tasks/broad/GermlineVariantDiscovery.wdl/#L140" [[diagnostics]] document = "broadinstitute/warp:/tasks/broad/GermlineVariantDiscovery.wdl" message = "GermlineVariantDiscovery.wdl:67:32: error: expected string, but found integer" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/tasks/broad/GermlineVariantDiscovery.wdl/#L67" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/tasks/broad/GermlineVariantDiscovery.wdl/#L67" [[diagnostics]] document = "broadinstitute/warp:/tasks/broad/Qc.wdl" message = "Qc.wdl:434:31: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/tasks/broad/Qc.wdl/#L434" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/tasks/broad/Qc.wdl/#L434" [[diagnostics]] document = "broadinstitute/warp:/tasks/broad/Qc.wdl" message = "Qc.wdl:436:46: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/tasks/broad/Qc.wdl/#L436" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/tasks/broad/Qc.wdl/#L436" [[diagnostics]] document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl" message = "UltimaGenomicsWholeGenomeGermlineTasks.wdl:814:27: error: expected string, but found integer" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L814" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L814" [[diagnostics]] document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl" message = "UltimaGenomicsWholeGenomeGermlineTasks.wdl:866:27: error: expected string, but found integer" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L866" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L866" [[diagnostics]] document = "broadinstitute/warp:/tests/cemba/pr/CheckCembaOutputs.wdl" message = "CheckCembaOutputs.wdl:1:1: error: a WDL document must start with a version statement" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/tests/cemba/pr/CheckCembaOutputs.wdl/#L1" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/tests/cemba/pr/CheckCembaOutputs.wdl/#L1" [[diagnostics]] document = "broadinstitute/warp:/verification/VerifyMetrics.wdl" message = "VerifyMetrics.wdl:87:89: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/verification/VerifyMetrics.wdl/#L87" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/verification/VerifyMetrics.wdl/#L87" [[diagnostics]] document = "broadinstitute/warp:/verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" message = "VerifyUltimaGenomicsWholeGenomeCramOnly.wdl:102:87: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl/#L102" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl/#L102" [[diagnostics]] document = "broadinstitute/warp:/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "VerifyUltimaGenomicsWholeGenomeGermline.wdl:161:87: error: a placeholder cannot have more than one option" -permalink = "https://github.com/broadinstitute/warp/blob/9b5e498e19b89ef72a2c27bb68884c54de768d76/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl/#L161" +message = "VerifyUltimaGenomicsWholeGenomeGermline.wdl:174:87: error: a placeholder cannot have more than one option" +permalink = "https://github.com/broadinstitute/warp/blob/0c6697b5b017be4f0335077f7807b67c091fdbac/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl/#L174" [[diagnostics]] document = "chanzuckerberg/czid-workflows:/workflows/index-generation/index-generation.wdl"