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Bundle Creation

Package WDL workflows with dependencies into ZIP files.

  • Auto-Detection

    Automatically finds all imported WDL files

  • Single File

    Creates a portable ZIP for submission

  • Import Resolution

    Resolves nested import paths

Quick Start

pumbaa bundle create --workflow FILE --output FILE

Flags

Flag Alias Required Description
--workflow -w Main WDL file
--output -o Output ZIP path

How It Works

flowchart LR
    A[Parse main WDL] --> B[Find imports]
    B --> C[Resolve paths]
    C --> D[Package to ZIP]
  1. Parses main WDL file
  2. Finds all import statements
  3. Resolves import paths
  4. Packages all files into ZIP

Example

Given workflow structure:

pipeline.wdl
tasks/
  alignment.wdl
  calling.wdl

pumbaa bundle create \
  --workflow pipeline.wdl \
  --output bundle.zip

pumbaa workflow submit \
  --workflow pipeline.wdl \
  --dependencies bundle.zip

See Also

  • Submit — Use bundles with submission