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Cromwell/WDL — Broad Institute workflow execution engine and WDL (Workflow Description Language) for defining, running, and scaling bioinformatics pipelines. Cromwell executes WDL workflows locally, o
Use with AI
Install the MCP server or CLI to instantly fetch Cromwell / WDL documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/cromwellwdl
Conda and Mamba package/environment management for bioinformatics. Create, export, and reproduce isolated software environments using conda or mamba (fast C++ solver). Manage Bioconda channels, resolv
2 shared topics • 1 shared operation
Dockstore — open platform for sharing Docker-based bioinformatics tools and workflows written in CWL, WDL, Nextflow, and Galaxy. Provides workflow discovery, versioned registrations, TRS API for progr
2 shared topics • 1 shared operation
Poetry is the Python dependency management and packaging tool for creating reproducible projects with pyproject.toml and poetry.lock. Use this skill for dependency resolution, virtual environment isol
2 shared topics • 1 shared operation
RTG Tools — Java-based toolkit from Real Time Genomics for haplotype-aware variant call comparison, VCF filtering, statistics, and pedigree analysis. Primary use: vcfeval for benchmarking variant call
2 shared topics • 1 shared operation
Wellcome Sanger Institute tools and resources — access COSMIC somatic mutation data, run Cancer Genome Project (CGP) WGS somatic variant calling pipelines (CaVEMan SNVs, Pindel indels, BRASS SVs, ASCA
2 shared topics • 1 shared operation