cbicall/Changes at main · CNAG-Biomedical-Informatics/cbicall · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
Revision history for cbicall:

1.1.0  Unreleased

    - Add standards-based Python packaging and installed CLI support.
    - Add a resource-free demo for WES audit and mtDNA browser reports.
    - Fix single-sample workflows to keep one sample name across FASTQs with different prefixes.
    - Fix mtDNA extraction from hg38 BAMs by selecting chrM instead of MT.
    - Migrate project documentation from MkDocs Material to Docusaurus.
    - Add a resource catalog, CBIcall bundle downloader, and runtime resource identity checks.
    - Add JSON Schema validation for the resource catalog.
    - Add runtime profiles for site-specific environment files, including CNAG HPC.
    - Add explicit registry versions and rename registry shared files from common to helpers.
    - Add native Nextflow and Cromwell support for GATK 4.6 WES/WGS workflows.
    - Add registered nf-core workflow support through the Nextflow backend, including demo and Sarek examples.
    - Add validate-parameters, validate-registry, validate-resources, test, compare-runs, and backend-equivalence checks.
    - Add run-report.json audit summaries with CBIcall version, workflow file hashes, software-version evidence, resource provenance, output file inventory hashes, output sizes, execution trace summaries, and output fingerprints.
    - Add text and HTML run comparison reports for two or more runs.
    - Extend run comparison with all-to-all matrices, VCF fingerprints, aliases, and MultiQC exports.
    - Add execution-contract audit files and generalize the workflow execution layer.
    - Add failed-run auditing and staged cohort execution for WES/WGS analyses.
    - Replace the legacy mtDNA report with an interactive variant browser.
    - Build Docker images from the checked-out source revision with provenance labels.
    - Rename workflow_engine/workflow_version YAML terminology to workflow_backend/workflow_provider.
    - Rename gatk_version YAML/report terminology to software_stack.

1.0.0  2026-03-23

    - First stable version released with pre-print.