New pipeline: nf-core/scalpel

[Franzx7]

Pipeline title/name

scalpel

Keywords

Isoform quantification with 3'tagged scRNA-seq data

What is it about?

Quantification of isoform usage and alternative polyadenylation (APA) from single-cell RNA-seq using a Nextflow-based pipeline

Please provide a schematic diagram of the proposed pipeline

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?

Innovative and benchmarked assessed new tool for Isoform quantification using 3'tagged scRNA-seq data. Enable characterization of alternative isoform at single-cell resolution and post-transcriptional regulation in cell-types.
published in Nature comms (https://www.nature.com/articles/s41467-025-61118-0)

Who would be interested?

Bioinformaticians, Researcher working with 3'tagged single-cell data

What has been done so far

The pipeline have been fully implemented using DSL2 syntax on Github (https://github.com/plasslab/SCALPEL).
I would like to make it suitable/available on nf-core.

URL to existing work (if applicable)

https://github.com/plasslab/SCALPEL

Are there any similar existing nf-core pipelines?

No response

[nf-core-bot]

Approval status: ✅ Approved

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

Review Status	Team members
✅ Approved (Core)	@jfy133, @mashehu
✅ Approved (Maintainer)	@nictru
🕐 Pending (Core)	@ewels, @maxulysse, @mribeirodantas, @JoseEspinosa, @mirpedrol, @FriederikeHanssen, @kenibrewer, @edmundmiller, @sateeshperi, @FranBonath, @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, @vagkaratzas, @sateeshperi, @jonasscheid, @famosab, @itrujnara, @LouisLeNezet, @Joon-Klaps, @jasmezz, @Felix-Kummer, @sofstam, @nvnieuwk

[akaviaLab]

I'm not a maintainer of any sort, but I have a question.
This looks very cool, and a defined pipeline. It also seems to have some overlap with rnasplice - what exactly is the overlap and can it re-use parts of rnasplice or vice versa? Is it like having rnaseq and scrnaseq as different workflows in nf-core?

Just curious about this, trying to understand how things work.

[jfy133]

I also don't immediately see any major overlaps with existing pipelines, so I'm inclined to accept (But I'm not an expert on transcirptomics). I would like to hear from more people working in the area.

[mirpedrol]

Tagging some of the developers/maintainers of the pipelines mentioned in the above comments. It would be great if you can give your feedback (or tag someone else), thanks!
@nictru @fmalmeida @grst @jma1991 @bensouthgate

[grst]

There is some overlap with scrnaseq (Salmon TPM quantification), but overall the pipeline serves too much of a different topic to be included in the scrnaseq pipeline. Would be great to rely on a common subworkflow for that part though, if possible.

[Franzx7]

Thanks all, I’m Franz, one of the core developer of SCALPEL.

There is indeed some conceptual overlap with rnasplice in the sense that both workflows deal with transcript diversity. However, the scope and methodology are totally different. SCALPEL is designed specifically for 3′-tagged scRNA-seq and implements statistical approaches designed for inferring isoform usage and APA-derived 3′UTR variation from single-cell data and have been published recently.

I’m currently rewriting SCALPEL into an nf-core–compliant pipeline (transitioning from DSL2 Nextflow to full nf-core structure). I expect this first version to be ready later this week or next week. Definitely in it, early steps of the pipeline that rely on salmon quant and salmon index will be derived for these existing pipelines

[jfy133]

I will give an initial /approval then while we wait for more feedback from the other commnity members

/approve

[jfy133]

@nictru @fmalmeida @jma1991 @bensouthgate reminder that it would be great to get your feedback here 🙏 (Sorry for the cross posting ;))

[fmalmeida]

Hi @jfy133 ,
Added on my list. As soon as I am back I will give it a read if still open :)

[fmalmeida]

Hi there,

It really seems that the only real overlap with scrnaseq is the quantification part as this pipeline really seems to focus on the post-processing with focus on the isoform results.

Would be only nice to have the quantification standardised across pipelines, for example as @grst mentioned to have a common subworkflow.

Maybe the post processing can also be a subworkflow?

I am thinking on the potential world where one executed scrnaseq for the "general" quantification and then can process the results with this pipeline. Would that be a possible scenario in your opinion?

Also, how much does it differ from the purpose of scdownstream? Would for example be a plausible scenario where the isoform work is added as a subworkflow there?

I am not saying it should or not, I just want to make sure we considered all the possibilities before deciding for one :)

[mashehu]

If things can be standardised between scrnaseq and scdownstream and this one you got my
/approve

But the name needs to be changed, something like scisoformquant?