`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 my.wdl.zip 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]
                   [--debug]
                   WDL_FILE

Positional Arguments

WDL_FILE: top-level WDL file

Named Arguments

-o, --output: destination filename [WDL_FILE.zip]
-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.

language

-p, --path: local directory to search for imports (can supply multiple times)
--no-outside-imports: deny local imports from outside directory of main WDL file (or –path)
--no-quant-check: relax static typechecking of optional types, and permit coercion of T to Array[T] (discouraged; for backwards compatibility with older WDL)

debugging

--debug: maximally verbose logging & exception tracebacks

miniwdl zip