Native Backends

CBIcall separates what analysis is run from how it is executed. Included Pipelines describes the shipped WES, WGS, and mtDNA analyses. This page describes backends used by CBIcall-native workflows. A workflow is native when it produces the CBIcall output contract, regardless of whether it is written in Bash, Snakemake, Nextflow, or WDL/Cromwell.

The workflow backend controls how the selected pipeline is launched.

Native backend	Role	Typical use
Bash	Runs CBIcall-maintained shell workflows directly	Production runs with the bundled WES, WGS, and mtDNA scripts
Snakemake	Runs CBIcall-maintained Snakemake workflows	Rule-based execution and partial workflow targets
Nextflow	Runs CBIcall-maintained Nextflow workflows	Alternative workflow-backend implementation for WES/WGS
Cromwell	Runs CBIcall-maintained WDL workflows	WES/WGS single-sample and cohort execution with Cromwell/WDL while preserving CBIcall audit outputs

Bash

The Bash backend runs CBIcall-maintained shell scripts from the workflows/bash directory. It is the broadest backend in CBIcall and includes WES, WGS, and mtDNA workflows.

Snakemake

The Snakemake backend runs CBIcall-maintained Snakefiles from workflows/snakemake. It supports WES/WGS workflows and is useful when rule selection or partial execution is needed.

Nextflow

The native Nextflow backend runs CBIcall-maintained Nextflow workflows from workflows/nextflow. It supports WES/WGS workflows and follows CBIcall's run directory and provenance model.

Cromwell

The Cromwell backend runs CBIcall-maintained WDL workflows from workflows/cromwell. Native support covers GATK 4.6 WES/WGS single-sample and cohort workflows. CBIcall generates Cromwell inputs/options JSON files, launches the registered WDL, and promotes final outputs into the standard 01_bam/, 02_varcall/, 03_stats/, and logs/ layout.

Use CROMWELL_JAR=/path/to/cromwell.jar or put a cromwell launcher on PATH before launching this backend. Optionally set WOMTOOL_JAR=/path/to/womtool.jar so validate-registry can run static WDL syntax checks.

CBIcall can also launch registered external nf-core workflows through Nextflow. Those workflows are documented separately because they keep their upstream output layout and runtime assumptions. See nf-core.

Backend-native validation

CBIcall validates the parameters YAML against the workflow registry and resource catalog, then writes a cbicall-execution-contract.json for the concrete command it launches. Syntax or semantic validation inside each workflow language remains backend-native: use bash -n for shell scripts, Snakemake lint/dry-run checks for Snakefiles, Nextflow's own validation for native Nextflow workflows, and womtool validate for WDL/Cromwell workflows.

Backend Selection

For CBIcall-native workflows, select the backend with workflow_backend:

pipeline:        wes
workflow_backend: bash
software_stack:    gatk-4.6

pipeline:        wes
workflow_backend: snakemake
software_stack:    gatk-4.6

pipeline:        wgs
workflow_backend: nextflow
software_stack:    gatk-4.6

pipeline:        wes
workflow_backend: cromwell
software_stack:    gatk-4.6

What to Read Next

Goal	Page
Run WES/WGS single-sample workflows	WES/WGS Single-Sample
Run WES/WGS cohort workflows	WES/WGS Cohort
Run mtDNA workflows	mtDNA
Run registered external nf-core workflows	nf-core
Add a new workflow entry	Adding a Pipeline