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v1.8.0

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@mlin mlin released this 25 Nov 08:23
· 66 commits to main since this release
  • In scatters, embed a string representation of the scatter variable in each call's logs and run subdirectory structure.
    • Facilitates identification of the call processing a given sample, but the string tag must be derived heuristically.
    • The tag length can be adjusted by config [scheduler] scatter_max_tag (0 to disable the new tagging).
  • Add config [file_io] use_relative_output_paths = true to flatten the out/ links structure. (#606 @rhpvorderman)
    • The generated link path relative to out/ reflects the path relative to the original task working directory.
    • Fails in the event of an output link path collision (e.g. a workflow outputting files with colliding names generated by different calls).
  • Fix out/ link directory structure for Maps (where subfolders used numeric indexes even if the map keys were suitable path components).
  • Fix postprocessing absent File?/Directory? task outputs. (#614 @rhpvorderman)
  • Fix parsing string literals ending with escaped backslash, e.g. "foo\\".
  • miniwdl zip: Fix archival of local WDL that imports a remote URI. (#610 @yunhailuo)

WDL version development features (experimental & subject to change)

  • openwdl/wdl#414 Multi-line strings: the <<< >>> task command delimiters can now be used to write multi-line string literals wherever needed.
  • openwdl/wdl#504 Support Defining Environment Variables Within a Task: task input declarations can be prefixed by the keyword env to bind the input as an environment variable for the command (an alternative to WDL command interpolations/placeholders).