fix: quote integer literals in placeholder default options - #1814
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claymcleod wants to merge 3 commits into
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fix: quote integer literals in placeholder default options#1814claymcleod wants to merge 3 commits into
default options#1814claymcleod wants to merge 3 commits into
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Placeholders in WDL cannot contain more than one option (e.g., `default` + `sep` or `true`/`false` paired with a second `default` + `sep` placeholder). This rewrites those expressions using `prefix()`, `sep()`, and `select_first()` to satisfy `sprocket lint` while preserving the original command-line output.
Placeholder options like `default` expect string values. Changes `default=0` to `default="0"` and `default=250` to `default="250"` across two task files.
claymcleod
marked this pull request as ready for review
April 11, 2026 15:31
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@claymcleod Thanks so much for this contribution and highlighting the syntax issue here. Unfortunately, we do not yet have tests for any of the AoU pipelines and cannot change them at this time. We will keep this open to revisit in the future. |
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Placeholder options like
defaultexpect string values per the WDL spec. This quotes the bare integer literals (default=0todefault="0",default=250todefault="250") inGermlineVariantDiscovery.wdlandUltimaGenomicsWholeGenomeGermlineTasks.wdl.Depends on #1812.