New pipeline: nf-core/starcaller

[Svenvdm]

Pipeline title/name

starcaller

Keywords

pharmacogenomics, star allele calling, diplotype calling

What is it about?

A pharmaocogenomics pipeline to call star alleles for a set of supported pharmacogenes from raw sequencing data. Important steps are read alignment, variant calling, star allele calling and post-processing of the results (reporting tool).

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?

Several tools have been developed to extract pharmacogenomic information from sequencing data. However, no comprehensive workflow currently exists that integrates all steps from read alignment through results reporting, nor is such a solution available in the nf-core community. StarCaller addresses this gap by providing an end-to-end pipeline for pharmacogenomic analyses.

Who would be interested?

Researchers/bioinformaticians working on pharmacogenomics.

What has been done so far

I have made a schematic overview of the pipeline architecture.

URL to existing work (if applicable)

No response

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)	@nvnieuwk, @jfy133
🕐 Pending (Core)	@ewels, @maxulysse, @mribeirodantas, @mashehu, @JoseEspinosa, @mirpedrol, @FriederikeHanssen, @kenibrewer, @edmundmiller, @sateeshperi, @FranBonath, @christopher-hakkaart
🕐 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

[mashehu]

cc @nvnieuwk, @maxulysse, @FriederikeHanssen

[nvnieuwk]

/approve

LGTM, but the first two parts of the workflow are already in Sarek, so either these parts should be removed or use the Sarek subworkflows to make development easier :)

[FriederikeHanssen]

Yep. We are trying to move towards having smaller pipelines that are compatible with each other in anticipation of pipeline chaining being possible. Could you envision developing this pipeline as a downstream pipeline of sarek and both of us working together to make the output compatible with your input?

[Svenvdm]

Hi @FriederikeHanssen & @nvnieuwk. I can see this pipeline working completely downstream of sarek. However, end-users would ideally run this pipeline as a standalone pipeline, without having to run sarek first (hence being an end-to-end pipeline). I'm not sure how that can be accomplished as of now? I was aware of the overlap with sarek and was definitely anticipating on using the Sarek subworkflows.

[nvnieuwk]

It's fine as long as you use the Sarek subworkflows for the preprocessing of the data. We are planning on splitting up pipelines in the future and being able to chain them together. So using the Sarek subworkflows will ensure that your pipeline is compatible with the Sarek output

[Svenvdm]

Using the Sarek subworkflows makes sense then, given the overlap with Sarek & future directions of pipeline chaining within nf-core pipelines. Thank you!

[jfy133]

If the plan is in the future to deprecate the mapping/variant calling once pipeline chaining is implemented, I do not see any overlaps with the final 'star allele calling' section with other pipelines so I give a

/approve

[jfy133]

I feel the name should be updated though, I don't think starcaller is descriptive enoguh, given there is the STAR RNA aligner...

Maybe pharmstarcaller or something like that, to indicate the target a bit more

[Svenvdm]

Hi @jfy133 thanks for the approval and your feedback on the name. The name starcaller was intended to be a placeholder name for now, as I guess the name can be changed later?