Bundle v1

CBIcall production workflows require a CBIcall-provided bundle containing third-party executables, reference genomes, known-sites files, interval lists, and auxiliary databases.

The current bundle is selected in the run YAML with:

resource: "cbicall-germline-resources-v1"

CBIcall resolves this key against the resource catalog, the JSON inventory of resource entries and their compatibility metadata:

resources/cbicall-resource-catalog.json

The resource catalog supports several resource types. Packaged workflows use the CBIcall-provided bundle described below.

The scripts/download_cbicall_bundle.py utility installs CBIcall bundle entries from the resource catalog. It uses the local catalog when available and otherwise retrieves the canonical catalog. It does not install arbitrary local or third-party resource layouts.

Bundle Identity

Field	Value
Resource key	cbicall-germline-resources-v1
Version	v1

Why this is explicit

The resource key is the identifier users select with resource. log.json records this key, the resource version, and a catalog fingerprint, so two runs can be checked for the same declared external dependency set.

Bundle Scope

This bundle supplies the external tools and reference data used by the cbicall-core workflows. See the canonical compatibility matrix for supported pipelines, modes, software stacks, and backends.

CBIcall checks compatibility using the exact versioned workflow keys declared in the resource catalog, for example nextflow/wgs/cohort/gatk-4.6/v1. External nf-core workflows manage their own dependencies and do not use this bundle.

Downloaded Files

The production bundle is distributed as a small identifier JSON, split archive parts, and a checksum file.

File	Purpose
cbicall-resource-id.json	Declares the resource key and is pinned by SHA-256 in the catalog.
data.tar.gz.md5	MD5 checksum file. The current bundle records the split archive parts.
data.tar.gz.part-00	Split archive part.
data.tar.gz.part-01	Split archive part.
data.tar.gz.part-02	Split archive part.
data.tar.gz.part-03	Split archive part.
data.tar.gz.part-04	Split archive part.
data.tar.gz.part-05	Split archive part.

The setup utility verifies the files covered by data.tar.gz.md5. For the current bundle, this means the split archive parts are checked before they are reassembled and extracted.

An optional small remote identifier file can also be used:

{"resource_key": "cbicall-germline-resources-v1"}

When available, this file is named cbicall-resource-id.json. Its SHA-256 can be pinned in the local catalog to confirm that the remote bundle declares the expected resource key.

Expected Layout

After extraction, DATADIR should contain:

DATADIR/
  Databases/
  NGSutils/

The bundle layout uses these conventional top-level names:

Variable	Meaning
CBICALL_DATA	User-facing environment variable that selects the installed bundle root for all native backends.
DATADIR	Root of the installed CBIcall-provided bundle.
DBDIR	DATADIR/Databases
NGSUTILS	DATADIR/NGSutils

CBIcall resolves CBICALL_DATA into the backend-specific DATADIR/datadir value. Workflow files such as Bash env.sh and Snakemake/Nextflow/Cromwell config.yaml then resolve the bundle layout into concrete executable and reference paths. Packaged workflow files should not be edited to select an installation directory.

Tools

Tool	Version	Path hint
GATK 4	4.6.2.0	NGSutils/gatk/gatk-4.6.2.0/gatk
BWA	0.7.18	NGSutils/bwa-0.7.18/bwa
Samtools	0.1.19	NGSutils/samtools-0.1.19/samtools

note

Some workflow branches may use architecture-specific executable paths or legacy tool paths. The catalog records the intended bundle identity; the workflow logs and log.json record the concrete paths resolved during a run.

If a bundled executable does not run

The bundle includes precompiled executables for both amd64 and arm64 architectures. They run on many common Linux distributions, but some older tools, such as BWA or Samtools, may depend on libraries that are not available on a particular system.

If this happens, rebuild the same pinned version in a separate, site-specific directory and select it through the institutional runtime profile. Run the relevant integration test before using it in production.

You can also use another tool version already provided by the system, for example through an HPC module. Keep in mind that even small version or build differences can change analytical outputs, including variant counts and test hashes. This does not necessarily mean that the workflow is wrong, but the user is responsible for validating the local tool setup before production use.

Reference Resources

b37

Resource	Path hint
Reference FASTA	Databases/GATK_bundle/b37/references_b37_Homo_sapiens_assembly19.fasta
dbSNP	Databases/dbSNP/human_9606_b144_GRCh37p13/All_20160408.vcf.gz
Mills / 1000G INDELs	Databases/GATK_bundle/b37/b37_Mills_and_1000G_gold_standard.indels.b37.vcf.gz

hg38

Resource	Path hint
Reference FASTA	Databases/GATK_bundle/hg38/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta

rsrs / mtDNA

The mtDNA workflows use MToolBox-related mitochondrial files from the bundle.

Provenance in Runs

The selected resource bundle is stored in log.json under config.resources.bundle.

Example:

{
  "key": "cbicall-germline-resources-v1",
  "compatible": true,
  "fingerprint": "..."
}

Two runs used the same declared external dependency set when their config.resources.bundle.fingerprint values match.

Installation Manifest

The setup utility also writes:

cbicall-resource-installation.json

This local manifest records the installed resource key, archive checksum result, source files, extraction status, and optional remote identifier provenance.

Runtime Check

Before launching a native workflow, CBIcall resolves the bundle directory from CBICALL_DATA. If the variable is unset, the selected institutional profile or backend configuration provides the fallback. CBIcall passes the resolved value to Bash, Snakemake, Nextflow, or Cromwell without modifying packaged files.

If bundle metadata exists beside DATADIR, CBIcall validates it:

File	Runtime check
cbicall-resource-id.json	Resource key must match the selected resource; SHA-256 must match the catalog when pinned.
cbicall-resource-installation.json	Installed resource key must match the selected resource; the manifest catalog entry must match the local catalog fingerprint.

This check is intentionally small. It validates the installed bundle identity without hashing the full resource archive on every run.