miniwdl
  • Getting Started
  • miniwdl run command line
  • miniwdl run reference
  • miniwdl run optimization
  • miniwdl run container runtimes
  • miniwdl check
  • miniwdl input_template
  • miniwdl zip
  • FAQ for miniwdl
  • Python WDL package
  • Python codelabs
miniwdl
  • miniwdl
  • View page source

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

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