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Matvii Mykhailichenko •
Forum: Interest in an on-premise automated pipeline for proprietary vendor sequencing data (e.g. Illumina)?
In our diagnostic routine at the Institute of Human Genetics, Medical University of Graz, I developed an automated on-premise pipeline for coordinating Illumina sequencing workflows. It integrates Illumina’s own on-prem software (DRAGEN from BCLs/FASTQs) and handles the surrounding automation - directory monitoring, staging, logging, notifications, and execution of the full workflow.
Before spending more time on polishing and generalizing it for release as an open GitHub repository, I wanted to ask whether the community would find such an on-prem DRAGEN-centered automation pipeline useful, either in diagnostic or research settings.
Short yes/no answers or brief comments are very welcome.
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Jeremy Leipzig
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Matvii Mykhailichenko •
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Matvii Mykhailichenko •
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Vendor software is integrated directly
Can you clarify if this software is integrating bcl-convert used for post-processing of data off-sequencer or DRAGEN (tied to the sequencer hardware, which not everyone may have access to or use).
while the pipeline manages directory monitoring, logging, notifications, and overall workflow execution.
So is this more like a LIMS?
I wanted to ask whether the community would find such an on-premise solution useful in diagnostic or research settings.
The utility is likely limited, even for research unless a lab is starting from scratch and can set up processes to follow the SOP used at your institution. For diagnostics, because of local policy/regulations (and custom software), not likely.
Edit: While I was composing this, OP provided additional clarification in a comment above. Sounds like this uses Illumina supplied on-prem DRAGEN server.
You could release the software with minimal polishing (but with clear directions) so it could be useful to someone who is starting out with on-prem DRAGEN server.
I think it is useful and interesting as well, would be good to see the software out there.
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colindaven
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How is it different from existing pipelines, e.g. nf-core and snakepipes?
It's python3 + some packages, as illumina doesn't allow to install third party software on on-premise servers (or we lose warranty)
So it won't run on any non-illumina supplied machine? I think most users would prefer to run pipelines independently on their cluster - and like you say, that may avoid warranty issues.
It does run on regular clusters, one only needs to adjust the command used to launch the pipeline. The reason I developed it this way is that many smaller centres rely on Illumina-supplied on-premise servers and cannot install third-party tools there due to warranty restrictions. For them, having an automated wrapper that orchestrates the vendor software plus directory monitoring/logging is useful. Larger centres with established HPC infrastructure and existing nf-core-style pipelines would probably prefer their own cluster-based workflows
Anything that complements DRAGEN in this way sounds like a good idea