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Move file virtualization in toil-wdl-runner to task boundaries #5028
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Move file virtualization in toil-wdl-runner to task boundaries #5028
Commits on Jul 19, 2024
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Defer file virtualization to task boundaries and consolidate decl eva…
…luation. Also gets rid of monkeypatching in favor of a manual function call
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Commits on Jul 24, 2024
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Implement support for importing relative URL paths; import files at s…
…tartup and carry through mappings
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Merge branch 'master' of github.com:DataBiosphere/toil into issues/50…
…04-wdl-virtualize-only-at-task-boundaries
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Get rid of sentinel value implementation + drop files before virtuali…
…zation in TaskWrapper for MiniWDL parity
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Commits on Jul 25, 2024
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Drop missing files during decl eval for outputs + Add a check for inv…
…alid coerced-to-null files and raise if exception found
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Commits on Aug 20, 2024
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Commits on Aug 22, 2024
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Commits on Aug 23, 2024
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Merge branch 'master' of github.com:DataBiosphere/toil into issues/50…
…04-wdl-virtualize-only-at-task-boundaries
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Commits on Aug 27, 2024
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Merge branch 'issues/5004-wdl-virtualize-only-at-task-boundaries' of …
…github.com:DataBiosphere/toil into issues/5004-wdl-virtualize-only-at-task-boundaries
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Commits on Aug 29, 2024
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Resolve nested virtualize files issue by converting back to original …
…and permanent devirtualization of URLs
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Merge branch 'master' of github.com:DataBiosphere/toil into issues/50…
…04-wdl-virtualize-only-at-task-boundaries
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Commits on Aug 31, 2024
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Fix virtualize/devirtualize_filename to be called only during command…
… stdlibs and combine_bindings issue with new virtualization representation
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Commits on Sep 3, 2024
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Commits on Sep 6, 2024
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Commits on Sep 10, 2024
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Commits on Sep 12, 2024
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Commits on Sep 16, 2024
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Commits on Sep 17, 2024
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Apply suggestions from code review
Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>
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Commits on Sep 18, 2024
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Update src/toil/wdl/wdltoil.py
Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>
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Merge branch 'issues/5004-wdl-virtualize-only-at-task-boundaries' of …
…github.com:DataBiosphere/toil into issues/5004-wdl-virtualize-only-at-task-boundaries
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Commits on Sep 19, 2024
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Commits on Sep 24, 2024
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Merge remote-tracking branch 'upstream/issues/5004-wdl-virtualize-onl…
…y-at-task-boundaries' into issues/5004-wdl-virtualize-only-at-task-boundaries
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Commits on Sep 26, 2024
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Commits on Sep 27, 2024
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Extract out the import function to add back memoization and resolve i…
…ssue of multiple imports on the same file
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Merge remote-tracking branch 'origin/issues/5004-wdl-virtualize-only-…
…at-task-boundaries' into issues/5004-wdl-virtualize-only-at-task-boundaries
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Merge branch 'master' of github.com:DataBiosphere/toil into issues/50…
…04-wdl-virtualize-only-at-task-boundaries
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