Version Compatibility

Reference examples tested with: BWA 0.7.17+, FastQC 0.12+, GATK 4.5+, Nextflow 23.10+, Salmon 1.10+, Snakemake 8.0+, fastp 0.23+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

WDL Workflows

"Build a WDL pipeline for Terra/AnVIL execution" → Define tasks and workflows in WDL (Workflow Description Language) for execution on Cromwell, miniwdl, or cloud platforms (Terra, AnVIL) with built-in GATK best practices support.

• CLI: cromwell run workflow.wdl or miniwdl run workflow.wdl for execution
• WDL: version 1.0 task/workflow syntax with scatter-gather parallelism

Basic Task Definition