[RESOLVED] What is happening to all pipelines from Parabricks v3 to v4?

Healthcare & Life Sciences Parabricks
1

Pipelines vanished from Parabricks v4 documentation… 🤔

Happily some are still available in nvcr.io/nvidia/clara/clara-parabricks:4.3.1-1 docker image, but will they be further developed or will they be deprecated?

Still available (but without docs):

command options for commonly used FULL PIPELINES

deepvariant_germline    - Run the germline pipeline from FASTQ to VCF using a deep neural network analysis
pacbio_germline         - Run the germline pipeline from FASTQ to VCF by aligning long read sequences with minimap2 and using a deep neural network analysis
germline                - Run the germline pipeline from FASTQ to VCF
somatic                 - Run the somatic pipeline from FASTQ to VCF

Not available anymore:

human_par
population studies pipeline
2

Hi @khamenya, the human par and population studies pipelines are deprecated.

3

thank you for reply, @gburnett.

OK with these two.

And what about others? it’s quite noticeable that the pipeline doc entries from v3 didn’t migrate to v4 docs. It’s not v4.0.0 anymore. It is already v4.3.1 .
What is the future of pipelines in/after v4?

UPDATE: nevermind! I found the new doc home for the legacy pipelines:
https://docs.nvidia.com/clara/parabricks/4.3.1/toolreference.html
in particular, e.g.
https://docs.nvidia.com/clara/parabricks/4.3.1/documentation/tooldocs/man_germline.html