New pipeline: nf-core/episegmixflow

[aaryanjaitly]

Pipeline title/name

episegmix_flow

Keywords

HistoneModifications, Chromatin States, Genome Segmentation, Epigenomics

What is it about?

This pipeline makes chromatin segmentation with EpiSegMix much easier and more accessible. It takes care of the tricky steps, like data formatting and parameter setup, so researchers can focus on their analysis. The EpiSegMix currently supports four different segmentation strategies: duration-based segmentation, standard non-duration segmentation, DNA methylation specific segmentation, and an automated distribution-fitting workflow (still in development).
The scope of this pipeline is strictly limited to EpiSegMix, though we plan to support other segmentation methods in a separate, dedicated workflow.

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?

There is currently no dedicated chromatin segmentation pipeline on nf-core, so this would be a pioneering addition. Beyond just running the tool, the main challenge for researchers is often the difficult process of formatting raw data into the correct input for segmentation models. This pipeline automates that entire struggle, making advanced chromatin modeling accessible to anyone with a single command.

Who would be interested?

Epigenomic researchers, bioinformaticians, and core facilities looking for an easy, automated way to create chromatin state maps.

What has been done so far

A functional Nextflow pipeline already exists that runs EpiSegMix and produces results using Docker and Singularity containers. Currently, only one workflow of EpiSegMix is implemented, and the pipeline has only been tested on hg38 and hg19. While it produces results, the tool is not yet fully robust, and much work remains, including adding the other workflows, extensive testing, and final polishing.
The groundwork is in place, and the next steps will focus on porting this prototype into the official nf-core template and refining it for a community-ready release.

URL to existing work (if applicable)

No response

Are there any similar existing nf-core pipelines?

No response

[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, @FriederikeHanssen, @kenibrewer, @jfy133, @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, @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, @FriederikeHanssen, @kenibrewer, @jfy133, @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, @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, @FriederikeHanssen, @kenibrewer, @jfy133, @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, @nictru, @itrujnara, @LouisLeNezet, @Joon-Klaps, @jasmezz, @Felix-Kummer, @sofstam, @nvnieuwk

[itrujnara]

I am not familiar with the analysis, so I cannot judge the proposal on the merits. However, from a quick search, it seems to be a novelty for nf-core. I have a slight doubt about the name: does the flow refer to some feature of the proposed pipeline, or is it just a reference to Nextflow/workflow? If it is the latter, I recommend using the name episegmix (cf. rnaseq, chipseq, and other pipelines for established methods).

[aaryanjaitly]

@itrujnara Yes, Flow was with respect to Nextflow only, and yeah, I also feel that keeping just episegmix is more comfortable.