miniwdl

miniwdl is a local runner and developer toolkit for the bioinformatics-focused Workflow Description Language (WDL).

• Getting Started
  • Install miniwdl
  • Fetch viral-pipelines
  • Run assemble_refbased workflow
  • Inspect results
  • Next steps
• miniwdl run command line
  • Positional Arguments
  • input
  • output
  • logging
  • configuration
  • language
  • debugging
• miniwdl run reference
  • I/O and run directory structure
  • Task runtime attributes
  • File & Directory URI downloads
  • Configuration
  • Using NVIDIA GPU
  • WDL interoperability
• miniwdl run optimization
  • WDL guidelines
  • Host configuration
• miniwdl run container runtimes
  • Podman (BETA)
  • Singularity (BETA)
  • udocker (BETA)
  • External plugins
• miniwdl check
  • Suppressing warnings
  • Pre-commit hook
  • Command line
• miniwdl input_template
  • Command line
• miniwdl zip
  • Command line
• FAQ for miniwdl
  • Common Questions
• Python WDL package
  • load()
  • load_async()
  • read_source_default()
  • resolve_file_import()
  • values_from_json()
  • values_to_json()
  • Tree
  • Expr
  • Env
  • Type
  • Value
  • Error
  • Lint
  • Zip
  • runtime
• Python codelabs
  • Syntax tree traversal
  • wdlviz
  • Adding WDL functions
  • WDL assertion statements

Links

• miniwdl repo for installation instructions & issue tracker

• OpenWDL repo for WDL spec, proposals, and discussion

• CZI Science Technology sponsors this project

Indices and tables

• Index

• Module Index

• Search Page