Included Pipelines
This page summarizes the analysis pipelines CBIcall can launch and the backend combinations currently supported.
| Concept | YAML key | Meaning |
|---|---|---|
| Pipeline | pipeline | The analysis family: wes, wgs, mit, or a registered external pipeline such as sarek. |
| Mode | mode | The run shape, usually single or cohort. |
| Workflow backend | workflow_backend | The execution technology: Bash, Snakemake, Nextflow, or Cromwell. |
| Workflow provider | workflow_provider | Who supplies the implementation: cbicall for native CBIcall pipelines, nf-core for registered external provider entries. |
A pipeline implementation is native when it produces the CBIcall output contract: standard run directory, logs, reports, output inventory, and final-output fingerprints when available. External provider entries can still be launched and audited by CBIcall, but they keep their upstream output layout and runtime assumptions.
Pipeline Guides
| Goal | Page |
|---|---|
| Process one WES/WGS sample from FASTQ | WES/WGS Single-Sample |
| Joint-genotype a WES/WGS cohort from gVCFs | WES/WGS Cohort |
| Run mitochondrial variant calling | mtDNA |
| Run selected external nf-core provider entries | External nf-core |
For a backend-centered view, see Native Backends.
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, Snakemake lint/dry-run checks, Nextflow validation,
or womtool validate for WDL/Cromwell workflows.
Compatibility Matrix
Native CBIcall workflows
| Pipeline | Mode | Genome | Software stack | Bash | Snakemake | Nextflow | Cromwell |
|---|---|---|---|---|---|---|---|
| WES | single | b37 | gatk-3.5, gatk-4.6 | V | gatk-4.6 | gatk-4.6 | gatk-4.6 |
| WES | cohort | b37 | gatk-3.5, gatk-4.6 | V | gatk-4.6 | gatk-4.6 | gatk-4.6 |
| WGS | single | b37, hg38 | gatk-4.6 | V | V | V | gatk-4.6 |
| WGS | cohort | b37, hg38 | gatk-4.6 | V | V | V | gatk-4.6 |
| mtDNA | single | rsrs | gatk-3.5 | V | X | X | X |
| mtDNA | cohort | rsrs | gatk-3.5 | V | X | X | X |
CBIcall does not ship a validated gatk-3.5 WGS workflow; native WGS support is provided through the gatk-4.6 stack.
The bundled mtDNA workflow is not supported on ARM / aarch64 because of legacy third-party dependencies.
Registered external workflows
| Pipeline | Mode | Registry source | Release | Resource model |
|---|---|---|---|---|
demo | single | nf-core/demo | 1.1.0 | Nextflow/nf-core managed |
sarek | cohort | nf-core/sarek | 3.8.1 | Nextflow/nf-core managed |