Cwl Python Packages

cwltool

Common Workflow Language reference implementation

cwl-utils

Python utilities for CWL

rocrate

Python library for RO-Crate

cwl-upgrader

Upgrade CWL syntax to a newer version

cwltest

Framework for testing CWL tools and workflows

toil

A WDL, CWL and Python API supporting easy-to-use workflow engine. It is scalable, efficient and cross-platform (Linux/macOS).

galaxy2cwl

Standalone version tool to get cwl descriptions (initially an abstract cwl interface) of galaxy workflows and Galaxy workflows executions.

cwl-runner

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

cwl-loader

Simple utilities to load CWL documents in a transparent way

arctrl

Polyglot (.NET/JS/Python) library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtime-agnostic contract systems.

tibanna

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

cwlref-runner

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

cwl2ogc

Convert CWL inputs and outputs into OGC API – Processes descriptors and JSON Schemas with Transpiler-Mate.

cwlprov

cwlprov: Command line tool and Python API to explore Research Objects containing provenance of Common Workflow Language executions

cwl2puml

Generate PlantUML diagrams from CWL workflows, with optional PNG and SVG rendering, using Transpiler-Mate.

cwlformat

A very opinionated code formatter for CWL

janis-pipelines

[Alpha] Janis: an open source tool to machine generate type-safe CWL and WDL workflows

cwl2click

Boostrap a Python CLI using click from a CWL CommandLineTool

cwl2ogcrecords

Generate OGC API – Records catalog metadata from CWL workflows with Transpiler-Mate to support discovery and reuse.

cwl2markdown

Generate Markdown documentation from CWL workflows and their software metadata with Transpiler-Mate.

cwl-baseline-plugin

Compare CWL releases, detect breaking changes, and check semantic version increments with explainable compatibility reports.

cwl2ro-crate

Package CWL workflows as Workflow RO-Crates and CWLProv execution records as Provenance Run Crates with Transpiler-Mate.

cwl2citation

Generate CFF, BibTeX, RIS, CSL-JSON, and styled citations from CWL workflow metadata with Transpiler-Mate.

cwl2sbom

Generate workflow and container CycloneDX SBOMs with Trivy for downstream offline supply-chain assessment.