Native Backends
CBIcall separates what analysis is run from how it is executed. The
analysis is selected with pipeline and mode; the execution technology is
selected with workflow_backend.
A pipeline implementation is CBIcall-native when it produces the CBIcall output contract:
the generated cbicall_* run directory, standard logs, audit reports, output
inventory, and final-output fingerprints when available. Native status is about
that output contract, not the workflow language.
Supported Native Backends
| Native backend | Current native role |
|---|---|
| Bash | Broadest native backend; includes WES, WGS, and mtDNA pipelines. |
| Snakemake | Native WES/WGS implementation for rule-based execution and partial targets. |
| Nextflow | Native WES/WGS implementation that follows the CBIcall run layout. |
| Cromwell | Native WDL implementation for GATK 4.6 WES/WGS pipelines. |
External nf-core provider entries are different: they are launched through the Nextflow backend, but they keep their upstream nf-core output layout and runtime assumptions. See External nf-core.
Selecting a Backend
pipeline: wes
mode: single
workflow_provider: cbicall
workflow_backend: bash
software_stack: gatk-4.6
For native pipeline implementations, workflow_provider: cbicall is the default. Change
workflow_backend to snakemake, nextflow, or cromwell when the selected
pipeline/mode/software stack supports that backend.
Use Included Pipelines for the compatibility matrix and pipeline-specific guides.