fix: convert draft-2 WDL files in all_of_us/rna_seq/GTEx/ to version 1.0 - #1815
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fix: convert draft-2 WDL files in all_of_us/rna_seq/GTEx/ to version 1.0#1815claymcleod wants to merge 4 commits into
all_of_us/rna_seq/GTEx/ to version 1.0#1815claymcleod wants to merge 4 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.
…n 1.0
Adds `version 1.0` declarations, wraps inputs in `input {}` blocks,
and changes `cpu` runtime values from strings to bare `Int` variables
across seven task/workflow files.
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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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Seven task/workflow files in
all_of_us/rna_seq/GTEx/were still using draft-2 WDL syntax (no version statement, bare inputs outside ofinput {}blocks). This converts them to WDL 1.0 by addingversion 1.0declarations and wrapping inputs ininput {}blocks. The existing${}placeholder syntax andcommand { }blocks are preserved since they're still valid in 1.0.Also changes the
cpuruntime key from a string (e.g.,cpu: "${num_threads}") to a bareInt(e.g.,cpu: num_threads) across all six task files, future-proofing for when runtime keys are formally typed (same strategy as #1811).Depends on #1814.