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 | Which collection supplies the implementation: cbicall-core for CBIcall's bundled native workflows, or nf-core for registered external 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. cbicall-core identifies the native workflow collection distributed
with CBIcall. 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.
Compatibility Matrix
Bundled workflows (cbicall-core)
Each backend cell shows the available GATK stack. X means that cbicall-core
does not provide that pipeline/backend combination.
| Pipeline | Mode | Genome | Bash | Snakemake | Nextflow | Cromwell |
|---|---|---|---|---|---|---|
| WES | single | b37 | GATK 4.6GATK 3.5 | GATK 4.6 | GATK 4.6 | GATK 4.6 |
| WES | cohort | b37 | GATK 4.6GATK 3.5 | GATK 4.6 | GATK 4.6 | GATK 4.6 |
| WGS | single | b37, hg38 | GATK 4.6 | GATK 4.6 | GATK 4.6 | GATK 4.6 |
| WGS | cohort | b37, hg38 | GATK 4.6 | GATK 4.6 | GATK 4.6 | GATK 4.6 |
| mtDNA | single | rsrs | GATK 3.5 | X | X | X |
| mtDNA | cohort | rsrs | GATK 3.5 | X | X | X |
cbicall-core does not include a validated GATK 3.5 WGS workflow. Bundled WGS
support uses GATK 4.6.
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 |