miniwdl zip

miniwdl zip generates a ZIP file including a given WDL source code file and any other WDL files it imports. The ZIP file can be supplied directly to miniwdl run, which can extract it automatically.

$ miniwdl zip path/to/my.wdl
$ miniwdl run input1=value1 ...

Optionally, you can also include a JSON file with default workflow inputs. Any command-line arguments provided at runtime would be merged into (override) these defaults.

The ZIP file will include a MANIFEST.json identifying the top-level WDL and inputs JSON, if present. The manifest format follows that of Amazon Genomics CLI.

Command line

usage: miniwdl zip [-h] [-o ZIP_FILE] [-f] [--input JSON_OR_FILE] [-a FILE]
                   [-p DIR] [--no-outside-imports] [--no-quant-check]

Positional Arguments

WDL_FILE top-level WDL file

Named Arguments

-o, --output destination filename []
-f, --force overwrite existing file
--input, --inputs, -i
 input JSON to include as defaults
-a, --additional
 Additional files to include in the zip. Files will be included in the zip root. Can be supplied multiple times.


-p, --path local directory to search for imports (can supply multiple times)
 deny local imports from outside directory of main WDL file (or –path)
 relax static typechecking of optional types, and permit coercion of T to Array[T] (discouraged; for backwards compatibility with older WDL)


--debug maximally verbose logging & exception tracebacks