v3.3.0 release#286
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williamrowell merged 2 commits intomainfrom Apr 22, 2026
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amwenger
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- refactor: Update all workflows, tasks, and subworkflows for sprocket compatibility - reformat meta and parameter_meta - symlink most inputs into working directory - quote most filenames - bump: update HiPhase to 1.6.0 - bump: update pbmm2 to 26.1.0 - bump: update pb-StarPhase to 2.0.1 - bump: update Mitorsaw to 0.2.7 - bump: update Paraphase to 3.5.0 - bump: update MethBat to 0.17.0 - bump: update DeepVariant to 1.10.0 - refactor: rename Boolean gpu to Boolean use_gpu for clarity - feature: add option Boolean use_parabricks_deepvariant to use Parabricks 4.7.0-1 DeepVariant for small variant calling (equivalent to DeepVariant 1.9.0) - docs: add documentation for Parabricks DeepVariant - refactor: increase resource allocation for tasks that are not IO-bound - refactor: remove GitHub Actions - refactor: removing wdl-common submodule to reduce complexity
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We're adding the wdl-common submodule files directly to the repo to reduce complexity. For historical reasons, we'll need to keep the wdl-common repo, but users won't need to recursively clone for new versions. I hadn't properly stripped the submodule in the PR. It should be addressed in 240bdaa. |
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refactor: Update all workflows, tasks, and subworkflows for sprocket compatibility
bump: update HiPhase to 1.6.0
bump: update pbmm2 to 26.1.0
bump: update pb-StarPhase to 2.0.1
bump: update Mitorsaw to 0.2.7
bump: update Paraphase to 3.5.0
bump: update MethBat to 0.17.0
bump: update DeepVariant to 1.10.0
refactor: rename
Boolean gputoBoolean use_gpufor clarityfeature: add option
Boolean use_parabricks_deepvariantto use Parabricks 4.7.0-1 DeepVariant for small variant calling (equivalent to DeepVariant 1.9.0)docs: add documentation for Parabricks DeepVariant
refactor: increase resource allocation for tasks that are not IO-bound
refactor: remove GitHub Actions; we're now testing internally
refactor: removing wdl-common submodule to reduce complexity