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 |