Wdl Python Packages

miniwdl

Workflow Description Language developer tools & local runner

toil

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

sprocket-bio

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

pytest-workflow

Configure workflow/pipeline tests using yaml files.

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.

turbo-picard

Picard-compatible Rust tools for faster SAM/BAM/CRAM, VCF, duplicate-marking and sequencing-QC workflows.

wdl-aid

Automatic Input Documentation for WDL workflows

janis-pipelines

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

wdl-lsp

Rich IDE support for Workflow Description Language

cromshell

CLI for interacting with Cromwell servers

wdldoc

Create WDL documentation using Markdown.

toil-msk

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

methseq

Automation tool for high-throughput sequencing DNA methylation data

cromshell-draft-release

CLI for interacting with Cromwell servers

cromtool

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

sprocket-py

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

wdl2cwl

[Experimental] Workflow Definition Language (WDL) to CWL

toil-cwl-runner

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

wdl-viewer

A web-based visualization tool to view (inter and inner) dependencies of WDL workflows.