Miniwdl

[](https://pypi.org/project/miniwdl/) [](https://anaconda.org/conda-forge/miniwdl) **[Getting Started](https://miniwdl.readthedocs.io/en/latest/getting_started.html)**

Maintenance release:

* `miniwdl input-template`: add `--no-namespace` option to omit the top-level workflow name prefix
* fix download caching when config `[file_io] root` is used (https://github.com/miniwdl-ext/miniwdl-aws/issues/20 staskh)
* logging improvements and dependency updates

* WDL spec compatibility:
* `==` and `!=` accept optional operands (634 jdidion)
* fix resolution of imported struct type aliases when the original struct name is reused in current document (635 jdidion)
* WDL 1.1: allow placeholder options like `sep=` in string expressions outside of task commands (633 adamnovak)
* WDL 1.1: disable a few `version development` features that had been inadvertently enabled for `version 1.1` (multi-line strings and optional `call:` keyword)
* allow extra JSON keys initializing structs (524)
* fix bug in `WDL.Env.merge()` that could resurrect previously-shadowed bindings (637 adamnovak)
* `miniwdl zip --additional` to include any specified file(s) in the zip (641 rhpvorderman)

* Change singularity invocation from `singularity run` to `singularity exec` (628 adthrasher)
* WDL `version development`:
* Make the `input:` keyword optional in calls (https://github.com/openwdl/wdl/pull/524)
* `miniwdl check`: reduce spurious warnings on `env` task inputs used as environment variables instead of WDL interpolations (https://github.com/openwdl/wdl/pull/504)

- Two **potentially breaking changes**:
- Remove the default `-l` (login shell) flag that had been supplied to each task command bash interpreter starting in v1.5.3, but caused interoperability problems (603). New config options mentioned below can restore this flag if necessary.
- Disallow implicit coercions of `Boolean? Int? Float? File? Directory?` to (non-optional) `String`, which should never have been permitted (596). These had been subject to `miniwdl check` deprecation warning since v1.7.1. They will still validate with `--no-quant-check`.
- New config options (see [default.cfg](https://github.com/chanzuckerberg/miniwdl/blob/v1.9.0/WDL/runtime/config_templates/default.cfg))
- `[task_runtime] command_shell` and `[task_runtime] command_preamble` customize the task command bash interpreter. For example, to restore the login shell flag, set `[task_runtime] command_shell = /bin/bash -l` or environment `MINIWDL__TASK_RUNTIME__COMMAND_SHELL='/bin/bash -l'`
- `[file_io] chown` to opt-out of the post-task chown of the working directory
- `[podman] exe` to customize the invocation for the podman backend (for example, to remove sudo)
- Relax PyYAML version requirements (625 adamnovak)
- Improve MultipleDefinitions error messages (622 crabba)
- Allow underscores in the short tags used to identify each iteration of a scatter
- `miniwdl zip`: fix assertion error importing WDL from a sibling directory sharing a common basename prefix with the main directory

* 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)**

* https://github.com/openwdl/wdl/pull/414 Multi-line strings: the `<<< >>>` task command delimiters can now be used to write multi-line string literals wherever needed.
* https://github.com/openwdl/wdl/pull/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).