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fix: update broken relative imports in deprecated pipelines - #1813

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claymcleod wants to merge 3 commits into
broadinstitute:developfrom
claymcleod:fix/deprecated-import-paths
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fix: update broken relative imports in deprecated pipelines#1813
claymcleod wants to merge 3 commits into
broadinstitute:developfrom
claymcleod:fix/deprecated-import-paths

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@claymcleod

@claymcleod claymcleod commented Apr 11, 2026

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When files were moved into deprecated/pipelines/ starting in 784c460 (#1541) and further reorganized in 973e831 (#1646), the relative import paths weren't updated to account for the new directory depth. This fixes all 79 broken imports across 29 files.

Depends on #1812.

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.
When files were moved into `deprecated/pipelines/`, relative import
paths were not updated to reflect the new directory depth. This
fixes all 79 broken imports across 29 files.
@claymcleod

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I just realized these are all in the deprecated/ folder, so rather than fixing them, I'll just exclude them from the lint run.

@claymcleod claymcleod closed this Apr 11, 2026
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