A WDL, CWL and Python API supporting easy-to-use workflow engine. It is scalable, efficient and cross-platform (Linux/macOS).
β926Updated this week
Alternatives and similar repositories for toil
Users that are interested in toil are comparing it to the libraries listed below
Sorting:
- Common Workflow Language reference implementationβ362Updated this week
- Repository for the CWL standards. Use https://cwl.discourse.group/ for support πβ1,479Jan 8, 2026Updated last month
- Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale productβ¦β1,053Updated this week
- Specification for the Workflow Description Language (WDL).β844Feb 18, 2026Updated last week
- An open source platform for managing and analyzing biomedical big dataβ416Feb 21, 2026Updated last week
- Deprecatedβ101Aug 12, 2019Updated 6 years ago
- [Historical] Reproducible Analyses for Bioinformaticsβ106Mar 11, 2019Updated 6 years ago
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysisβ1,026Aug 24, 2024Updated last year
- Create cwl workflows by writing a simple Python scriptβ40Apr 29, 2020Updated 5 years ago
- A DSL for data-driven computational pipelinesβ3,307Updated this week
- Workflow Description Language developer tools & local runnerβ200Feb 8, 2026Updated 3 weeks ago
- Toil workflows for common genomic pipelinesβ33Oct 3, 2019Updated 6 years ago
- An app store for scientific workflows, tools, notebooks, and servicesβ131Feb 18, 2026Updated last week
- Implementation of the GA4GH Workflow Execution Service, a REST service for running workflowsβ38Feb 5, 2026Updated 3 weeks ago
- cython + htslib == fast VCF and BCF processingβ429Updated this week
- Bioinformatics containersβ776Feb 4, 2026Updated 3 weeks ago
- Fast fusion detection using kallistoβ79Jun 11, 2025Updated 8 months ago
- Standalone C library for assembling Illumina short reads in small regionsβ72Dec 15, 2022Updated 3 years ago
- A powerful workflow engine implemented in pure Pythonβ1,860Jan 15, 2026Updated last month
- A light-weight wrapper library around Spotify's Luigi workflow library to make writing scientific workflows more fluent, flexible and modβ¦β335Dec 10, 2024Updated last year
- Cloud-native genomic dataframes and batch computingβ1,049Updated this week
- CWL on Kubernetesβ52Feb 4, 2026Updated 3 weeks ago
- A language server for Common Workflow Languageβ66Dec 6, 2023Updated 2 years ago
- Efficient pythonic random access to fasta subsequencesβ482Sep 3, 2025Updated 5 months ago
- De novo assembly based variant calling pipeline for Illumina short readsβ110Nov 30, 2020Updated 5 years ago
- Simple pure Python SAM parser and objects for working with SAM recordsβ64Jun 21, 2022Updated 3 years ago
- Import a CWL workflow specification to Nextflow script (experimental)β27Aug 9, 2018Updated 7 years ago
- β36Aug 13, 2020Updated 5 years ago
- Interactive in-browser track viewerβ280Oct 26, 2021Updated 4 years ago
- A lightweight parallel task engineβ148Jul 1, 2020Updated 5 years ago
- A curated list of awesome pipeline toolkits inspired by Awesome Sysadminβ6,531Feb 9, 2026Updated 2 weeks ago
- Tools for working with genomic and high throughput sequencing data.β354Feb 17, 2026Updated last week
- Python package to extend Airflow functionality with CWL1.1 supportβ192Oct 25, 2023Updated 2 years ago
- Generation of CWL programmatically. Available types: CommandLineTool and DockerRequirementβ30Jun 9, 2020Updated 5 years ago
- [Legacy] Executor for CWL workflows. Executes sbg:draft-2 and CWL 1.0β75Nov 18, 2020Updated 5 years ago
- A flexible framework for rapid genome analysis and interpretationβ319Oct 18, 2022Updated 3 years ago
- fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"β304Nov 14, 2025Updated 3 months ago
- Microassembly based somatic variant caller for NGS dataβ154Jun 23, 2022Updated 3 years ago
- [Alpha] Janis: an open source tool to machine generate type-safe CWL and WDL workflowsβ44Sep 17, 2023Updated 2 years ago