Crate commonwl 

CommonWL

A Rust-framework for the Common Workflow Language (CWL) that supports parsing and execution.

Overview

commonwl is a Rust-based library crate supporting parsing and executing CWL Workflows and Tools. It is based on the headless task execution framework crankshaft. It is developed to being used in the Scientific Workflow Infrastructure (SciWIn). There is a conformance CLI which is being used to evaluate CWL Conformance.

Getting Started

Installation

To use commonwl, you need to install and setup a Rust environment. Once Rust is installed, you can add the latest version of commonwl be using the following command

cargo add commonwl 

To use the execution engine, the engine feature needs to be enabled!

commonwl = { version = "0.8", features = ["engine"] }

CWL Engine

The CWL Engine features high conformance to the specification, passing all Tests for Workflow and ExpressionTool and nearly all tests for CommandLineTool. The conformance is dependent on the used TaskBackend. Currently there are the following existing and planned backends:

Backend	Status	Overall Conformance
Local	✔️
Docker*	✔️
TES	🏗️	-
Slurm	🧾	-

✔️: Fully operational - 🏗️: Under Construction - 🧾: Planned

*=Uses Docker even if DockerRequirement is not specified.

Two tests fail due to f64 overflow outputting 1e42 instead of one with 42 zeros. serde_json stores all numbers as f64.

License

This work is dual-licensed under Apache 2.0 and MIT . You can choose between one of them if you use this work.

SPDX-License-Identifier: Apache-2.0 OR MIT

Funded by

DFG project number 501899475

Modules

documents

engineengine

files

format

inputs

outputs

packed

requirements

storageengine

types

validate

Macros

guard

Structs

FileMetaData

FilePathMetaData

Enums

BoolOrExpression

Error

Integer

IntegerOrExpression

NumberOrExpression

OneOrMany

Traits

ExtractFromEnum

Identifiable

Functions

docstring

from_str

Loads a CWLDocument from a string, may be packed or unpacked

get_file_metadata

Tries to retrieve FileMetaData for given Path

get_path_metadata

load_cwl_file

Loads and may preprocesses a CWLDocument from Disk

preprocess_cwl_file

Preprocesses the $import sections of CWL Files

value_as_string

Returns String, Number or Bool as String

Type Aliases

Result

Derive Macros

Identifiable

Derive Macro for Identifiable