New pipeline: dragen

[mikefeixu]

Pipeline title/name

dragen

Keywords

dragen, demultiplex, alignment, UMI

What is it about?

This project focuses on initiating [nf-core/dragen], a nf-core pipeline for processing illumina sequencing data with UMIs.

Please provide a schematic diagram of the proposed pipeline

What would a minimal first release of this pipeline include?

Modules of demultiplex, mergelane(optional), and alignment with/without UMI collappsing. It will generate collapsed (simplex, duplex, unfiltered), and uncollapsed (standarded) bam files.

I confirm my proposed pipeline will follow nf-core guidelines. Most importantly, my pipeline will:

• be built with Nextflow.
• pass nf-core lint tests and use standardized parameters.
• be community-owned and developed within the nf-core organization.
• open source under the MIT license with proper credits and acknowledgments.
• have a descriptive, all lowercase, and without punctuation name.
• use the nf-core pipeline template and predominantly use official nf-core modules.
• focus on a specific data/analysis type with appropriate scope.
• have properly maintained documentation.
• be bundled using versioned Docker/Singularity containers.

Why do we need a new pipeline?

Dragen pipeline doesn't exist so far. As dragen alignment is fast. It will be very helpful to users want to implement Dragen in their production envionment.

Who would be interested?

Researchers and other users who are working on illumiina sequencing data and own access to dragen servers(licensed).

What has been done so far

I have started making local modules for tools I would use in the proposed pipeline. Moving it to nf-core now.

URL to existing work (if applicable)

No response

Are there any similar existing nf-core pipelines?

none

[nf-core-bot]

Approval status: 🕐 Pending

Required approvals: Either 2 core team members OR 1 core team member + 1 maintainer

Review Status	Team members
🕐 Pending (Core)	@ewels, @maxulysse, @mribeirodantas, @mashehu, @JoseEspinosa, @mirpedrol, @matthdsm, @FriederikeHanssen, @kenibrewer, @jfy133, @atrigila, @edmundmiller, @awgymer, @SPPearce, @sateeshperi, @FranBonath, @LouisLeNezet, @christopher-hakkaart, @nvnieuwk
🕐 Pending (Maintainer)	@pontus, @maxulysse, @lpantano, @pinin4fjords, @mashehu, @JoseEspinosa, @mirpedrol, @GallVp, @FloWuenne, @matthdsm, @FriederikeHanssen, @adamrtalbot, @mahesh-panchal, @jfy133, @atrigila, @prototaxites, @ramprasadn, @edmundmiller, @luisas, @SPPearce, @camlloyd, @vagkaratzas, @sateeshperi, @jonasscheid, @famosab, @nictru, @itrujnara, @LouisLeNezet, @Joon-Klaps, @jasmezz, @Felix-Kummer, @sofstam, @nvnieuwk

[nf-core-bot]

Approval status: 🕐 Pending

Required approvals: Either 2 core team members OR 1 core team member + 1 maintainer

Review Status	Team members
🕐 Pending (Core)	@ewels, @maxulysse, @mribeirodantas, @mashehu, @JoseEspinosa, @mirpedrol, @matthdsm, @FriederikeHanssen, @kenibrewer, @jfy133, @atrigila, @edmundmiller, @awgymer, @SPPearce, @sateeshperi, @FranBonath, @LouisLeNezet, @christopher-hakkaart, @nvnieuwk
🕐 Pending (Maintainer)	@pontus, @maxulysse, @lpantano, @pinin4fjords, @mashehu, @JoseEspinosa, @mirpedrol, @GallVp, @FloWuenne, @matthdsm, @FriederikeHanssen, @adamrtalbot, @mahesh-panchal, @jfy133, @atrigila, @prototaxites, @ramprasadn, @edmundmiller, @luisas, @SPPearce, @camlloyd, @vagkaratzas, @sateeshperi, @jonasscheid, @famosab, @nictru, @itrujnara, @LouisLeNezet, @Joon-Klaps, @jasmezz, @Felix-Kummer, @sofstam, @nvnieuwk

[awgymer]

I think that there are some issues to be addressed here which were already raised elsewhere, the main one being how would this pipeline and its modules be tested because of the architecture and license requirements of DRAGEN?

There exists an example dragon pipeline from Seqera and I also wonder how much this project would overlap with that?

I think that whilst in theory I am not opposed to nf-core owning and maintaining pipelines which use tools requiring licenses we there are many hurdles to making it viable and worthwhile and we have in the past (with old ONT tools with restrictive licenses) taken the view that the friction of these things is too high to make it worth including in nf-core

[mikefeixu]

Thank you so much for your reply!

1. DRAGEN integration with Seqera Platform is currently only available for use on AWS, and maybe extended to other platforms like Azure in the future. It doesn't support user to run the pipeline with their own Dragen servers. Some user sensitive data (like PHI) has too be run locally.
2. DRAGEN integration with Seqera Platform with module --build-hash-table, which is only needed once to build the reference.
3. The proposed DRAGEN pipeliine supports alignment with/without UMI collappsing. It will generate collapsed (simplex, duplex, unfiltered), and uncollapsed (standarded) bam files when UMI is used.
4. Testing: We will only include stub tests. User will need to run the pipeline on their own DRAGEN server. I will test on our Dragen server to ensure it really works.

[mashehu]

nf-core builds on collaboration and not having an easy setup to test ones code will make this quite difficult imo.

[jfy133]

Yeah this is a tricky one, 'only stubs' isn't really ideal for various reasons - e.g. you can't have the example AWS Megatest results/ output for example... let's have more @nf-core/core input on this one... I'm in two minds

[awgymer]

I think personally I am against this because it breaks strongly from nf-core standards in that way. However I do think there is a space in the broader community for sort of "semi-open" pipelines/modules/subworkflows in this way and that it could be to the benefit of nf-core if we can find a space for these under our umbrella? That's probably a more in-depth discussion for core that would require more serious thought though?

[maxulysse]

For me if we cannot really test it, I don't see it fit here in nf-core.
Similar-ish tools I have in mind would be sentieon or parabricks, and we can effectively test these.
That being said, I see no problem for any Nextflow pipeline to exists outside of nf-core, as we're all part of the bigger Nextflow community, and we still aim to collaborate all together.