OncoTracer v1.1

OncoTracer v1.1

Stable research release with four clearly documented launch methods:

1. Nextflow with Docker (--docker)
2. Nextflow with Singularity or Apptainer (--singularity)
3. The Poetry-managed launcher (poetry run oncotracer)
4. Nextflow with native Conda environments (--conda)

QuickStart 1 and QuickStart 2 passed complete public-data validation through Docker, Poetry with Docker, and Conda on scientific-code commit 0f1a3d86521afcb5eac3ce6e65fd45d455e8c843. Final release commit 032c1268fa7fdcadc48087055066d7a9fc59bd89 adds documentation and documentation-regression coverage only; it does not change the scientific workflow code.

The documentation gives explicit Docker, Singularity/Apptainer, Poetry, and Conda commands in QuickStart 1, QuickStart 2, Automatic Setup, the complete PRJNA754199 tutorial, and the mock six-tumor/four-normal example.

Validation covered public-read integrity, Automatic Setup, SAMURAI, qDNAseq/ichorCNA, BAM refinement, CNA tables, plots, workflow summaries, BAM integrity, final output verifiers, portable Docker ownership, the Poetry launcher, native Conda environments, and the pinned local SAMURAI source cache.

Singularity/Apptainer uses the same maintained container image as Docker and is documented for configured HPC systems.

OncoTracer is for research use and is not a standalone diagnostic system.