nf-core/seqinspector aims to be a pipeline for initial quality control of sequencing data. Input is either FASTQ files or a run folder, and output is planned to be a global MultiQC report and, if wished, MultiQC files of groups that are defined in the sample sheet. By joining this group you can

1. add existing modules to a pipeline (beginner friendly)
2. write a new module of your preferred QC tool if it doesn’t exist yet (intermediate level).
3. start with implementation of long read methods (advanced level, we have only limited experience in the group, so help would be more than appreciated!).
4. work on display of the data in the MultiQC reports (beginner - intermediate level)
5. write documentation

Goal

Work towards a first release

Group Leaders

Franziska Bonath

nf-core/scrnaseq transforms FASTQ files into expression matrices, while nf-core/scdownstream receives expression matrices as input and performs quality control, integration, clustering and more. This project has two main parts:

1. Move some local modules from scdownstream to nf-core/modules so that they can be re-used in scrnaseq.
2. Add new features to scdownstream. See the open enhancement issues for details.

By joining this group you can:

1. Create new modules and move existing local modules to nf-core/modules (beginner friendly)
2. Integrate the newly added modules into the pipelines (beginner - intermediate level)
3. Improve the scdownstream MultiQC report and documentation (beginner - intermediate level)
4. Look into a potential extension of scdownstream to multi-omics analyses (advanced level, has not yet been tackled but help would be great!)

Prior experience with single cell analysis is not required, but helpful.

Goal

Move shared functionality to nf-core/modules and make #scdownstream ready for 1.0 release

Group Leaders

Nico Trummer

We proposed a new pipeline to nf-core, initially called STIMULUS (available here: https://github.com/mathysgrapotte/stimulus). This pipeline aims to explore ways that deep learning models can learn, relative to how the input data is processed (check GitHub or the #deepmodeloptim channel on the nf-core slack).

Working on deepmodeloptim on the hackathon will mostly involve nf-core-izing the pipeline and making it a place where it is easy to contribute.

Goal

Reach nf-core/deepmodeloptim v1.0.0 release!

Group Leaders

Mathys Grapotte

General work on sarek with a focus on maintenance:

• Improve input validation
• Improve documentation
• Fix bugs

If you want to get started on a new addition, this is a great time to come by and chat.

Goal

Improve input validation, usability, and docs

Group Leaders

Rike Hanssen

Variant calling has multiple time consuming steps that could be faster if we use GPUs instead of CPUs. First steps to achieve that could be the integration of Parabricks which is software developed by NVIDIA. The modules are ready and need to be integrated into sarek.

This project can also expand onto other pipelines and include more tools that allow execution on GPU.

Goal

Integration of Parabricks in sarek

Group Leaders

Eugenio Franzoso

Famke Bäuerle

A pipeline to compare and contrast genome assemblies and their annotations.

When you sequence a new genome, or wish to use a published genome, it is important to gauge the quality of the assembly. There are basic tools, such as BUSCO (completeness), QUAST (contiguity), or general statistics of numbers of chromosomes, genes, etc (AGAT), but no nf-core pipeline to perform all of these tasks, including documenting their TE content, telomere locations, contamination level.

In addition, we would want to plot this on a phylogenetic tree, to help compare these stats. See the #genomeqc nf-core Slack channel to join!

Goal

Write a first draft of this pipeline

Group Leaders

Chris Wyatt

Usman Rashid

Fernando Duarte

Mahesh Binzer-Panchal

This is a variant benchmarking pipeline, for now structural variant and small benchmarking parts for germlines are working, yet there are plans for addin g somatic benchmarking including creation of a truth file for structural variants and adding some benchmark tools. The pipeline needs to be tested extensively and a set of reviews is required.

Goal

I would like to have the first version of this pipeline published

Group Leaders

Kübra Narcı

We have adding new reporting capabilities to the pipeline lately and we would like to finish adding this features and testing them during the hackathon.

A part from this, we would like to explore which other tools could be added to the pipeline (e.g. RoseTTAFold or OmegaFold) and discuss with the community what should be the future of the pipeline in terms of development.

Of course, as any other pipeline we would try to find other more “house-keeping” issues in which people joining the group could get involved during the hackathon.

If you are interested please join the group!

Goal

Towards release 1.2.0 and beyond

Group Leaders

Jose Espinosa-Carrasco

This is a pipeline for downstream gene expression analysis, with a main focus on differential expression analysis. Currently, we are working on a new branch dev-ratio with two objectives:

• add new methods
• convert the pipeline into a modular and unified framework that allocates different ways of performing differential analysis.

By joining this group you will help with:

1. Implement and add nf-core modules that wrap other methods that can be used to perform differential analysis. Some modules (ie. propr) were already created but need to be updated (beginner friendly).
2. Add these new modules to the pipeline and update the pipeline parameters correspondingly (beginner friendly).
3. Add the existing modules to the new modular subworkflow in a way that will reproduce the original pipeline’s behaviour (beginner - intermediate level).
4. Update the code required to generate the plots and reports (beginner - intermediate level).
5. Help in the restructuring of the pipeline architecture (intermediate level).
6. Update documentation (beginner friendly).

Goal

finish the integration of new modules and work towards the restructuring of the pipeline

Group Leaders

Suzanne Jin

Björn Langer

Jonathan Manning

Oskar Wacker

This project focuses on creating modules and adding functionality to (highly multiplexed) imaging pipelines - nf-core/mcmicro and nf-core/molkart. By joining this group you can:

1. Create new segmentation modules for nf-core/modules (beginner friendly) …
2. … and integrate them into the pipelines (beginner - intermediate level)
3. Support the spot detection implementation for MCMICRO (intermediate level)
4. Work on improved QC metric reporting for both pipelines (beginner - intermediate level)
5. Help us address open issues (beginner - intermediate level)

Goal

Work towards next Molkart release and implement an additional MCMICRO segmentation option.

Group Leaders

Kresimir Bestak

We will work on updating the meta.yml file of subworkflows to have the proper description for the structure of input and output channels.

Check the issue describing the tasks and tracking the progress.

Beginners and first-time contributors are welcome!

Goal

Update the meta.yml file of all nf-core subworkflows

Group Leaders

Júlia Mir

Looking into making more packages build natively for linux/arm64 and improving performance of the important ones for faster and cheaper runs on ARM machines such as AWS Graviton.

Goal

Optimise run time on at least one tool

Group Leaders

David Lecomber

Continuing the discussion from last year’s hackathon, this group will work on tasks related to references’ genomes handling / management. Some work has started with nf-core/references but it is at a very early stage. This hackathon group will work towards agreeing on a fundamental structure and plan.

Goal

Replacing iGenomes, then world domination.

Group Leaders

Maxime Garcia

Jonathan Manning

Everybody loves the nf-core tube maps, but they also need some special care to gleam in all their beauty. Come join us and refine your workflows representations to their full glory. Doesn’t matter if you already have a finished version and want a thorough review (🦅👀) or brainstorm some ideas and concepts to start a new one, this group is for you. Disclaimer: This will not be an introduction to vector graphic tools. You bring the tools, we bring the eyes and brains.

Goal

Make the tube maps in pipelines even more fabulous.

Group Leaders

Matthias Hörtenhuber

nf-test is a very important piece of our modules, used for continuous integration testing of all our modules. However, writing tests for some file types / more advanced tests can be difficult. In this group we will try and kickstart the creation of nf-test plugins to make our testing a lot easier. This will mainly involve the development of nft-utils, the improvement of nft-bam and hopefully the creation of completely new nf-test plugins.

Goal

Fully develop nft-utils and start new nf-test plugins

Group Leaders

Nicolas Vannieuwkerke

This group will work on tasks for the #regulatory special interest group. Most likely we will try to come up with more detailed plans on how to tackle different needs of subgroups within regulatory and try to come up with a strategy on how to both align between those subgroups as well as to come up with plans / proposals for the wider community what we could add to enable e.g. auditors or authorities to understand better what nf-core already provides.

Goal

Clearing out the scope of the regulatory special interest group and discussing who would tackle different subfields of the entire regulatory space for future improvements on nf-core guidelines and pipelines.

Group Leaders

Alexander Peltzer

We will work together on any or all of the meta-omics pipelines — mag, ampliseq, metatdenovo, magmap, eager, funcscan, createtaxdb and taxprofiler etc. — extending functionality, but also discussing how they can be made to better integrate with each other plus a number of downstream pipelines, both within and outside nf-core.

We will have a number of documentation and/or new-module requests for newcomers to get their hands dirty, and larger implementation tasks for more advanced developers.

Goal

Widened understanding of the implementation details of all pipelines in a larger group of developers.

Group Leaders

Daniel Lundin

James Fellows Yates

nf-core pipelines are playing a crucial role in standardising bioinformatics workflows and their user base is growing every day. Engaging training materials are essential to complement the pipelines that are being released. To achieve this, a problem-based learning approach could be developed for several nf-core pipelines where tutorials follow a storyline based on carefully simulated data. A first attempt at this approach has been drafted for nfcore/sarek (https://lescai-teaching.github.io/sarek-tutorial) and nfcore/rnaseq (https://lescai-teaching.github.io/rnaseq-tutorial). This project intends to gather people who are willing to discuss and develop further similar materials for these and other nf-core pipelines.

Goal

Develop tailored course materials and hands-on tutorials.

Group Leaders

Lorenzo Sola

Mariangela Santorsola

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