Channels - the Nextflow podcast

In this episode of Channels, the Nextflow podcast, host Geraldine from Seqera and her colleague Ben Sherman dive into the differences and similarities between Nextflow and the Workflow Description Language (WDL). They discuss the origins and development of WDL at the Broad Institute, the challenges of working with different workflow languages, and how Nextflow's channel-based data flow model compares to WDL's approach. The conversation covers key features, type systems, and runtime specifications, highlighting the strengths and limitations of both languages. Ben hints at upcoming improvements and enhancements for Nextflow, aimed at making the language more robust and user-friendly. The episode offers valuable insights for bioinformaticians and developers navigating the complexities of workflow management.

In this episode of Channels, the Nextflow podcast, join us as we explore Nextflow and AI. Our special guest, Sasha from Seqera, shares his remarkable journey from the consumer tech industry to bioinformatics. Learn about the birth of TinyBio, its innovations in bioinformatics AI applications, and its recent acquisition by Seqera. We delve into AI concepts, the challenges faced, and the future of integrating AI with Nextflow. Tune in to discover how advancements in AI are reshaping the bioinformatics landscape.

In episode 44 of the Nextflow Channels podcast, Phil Ewels welcomes Alex Pelzer— a key figure in the Nextflow and nf-core community. Alex shares his journey from academia to the pharmaceutical industry, highlighting the critical role of regulatory frameworks in bioinformatics.

🌟 Key Highlights:

Alex also discusses the formation of the @nf-core Regulatory Special Interest Group, which aims to bring together experts in the field to establish and promote best practices for ensuring pipeline quality and compliance with regulatory standards.

Looking forward to seeing many of you at the upcoming #NextflowSummit in Barcelona this October! We’ll be working with this #regulatory group during the nf-core hackathon.

00:00 Episode 44: Regulatory revolution

In this episode we explore the new features of Seqera's Data Studios and Data Explorer, with Phil Ewels, Rob Newman and Rob Syme from Seqera.

Discover how to use these tools for troubleshooting Nextflow pipelines, tertiary analysis and Nextflow development. We discuss the pain points that led to the creation of Data Studios and how it's designed to allow scientists to interactively and collaboratively work with data and complex workflows, without having to move large datasets around.

Rob Syme wows us with another fantastic practical demonstration, setting up and using Data Studios to write and test a Nextflow pipeline in VSCode running on the cloud in a Data Studio environment, including running the Nextflow CLI with task submission to AWS Batch.

We cover features like session persistence to save work states, and upcoming custom container support for your own specialized applications.

Learn how these tools can enhance your computational biology projects and make seamless cloud integration a reality.

00:00 Channels Podcast 43: Data Studios

A small but intrepid team of Seqerans recently attended the ISMB 2024 conference in Montreal, a great mix of computational biology and bioinformatics with a largely academic / research-focused audience. Join Geraldine Van der Auwera, Rob Syme and Florian Wuennemann for a lively discussion about the scientific themes of the conference, their experience running the booth, meeting with the ISMB and BOSC community, and resources for job seekers.

Join us in exploring the latest Nextflow release, 24.04. Phil Ewels and Ben Sherman dive deep into the new updates in Nextflow’s most recent version. We discuss advanced retry strategies, job arrays, resourceLimits, Singularity’s OCI mode, and the game-changing Workflow Output Definition.

We’re actively seeking feedback from the community on these new features. We would love for you to experiment with the new syntax and let us know your thoughts.

Please let us know what you think either via Nextflow GitHub issues or via the community forum.

In this episode we refer to a the recent blog post about the release, which you can find here: Nextflow 24.04 - Release highlights.

Intro - tweaks, fixes and new support in 24.04

Performance and Stability Improvements

Ben kicks off the discussion with key performance and stability improvements. The latest stable release, 24.04, includes numerous bug fixes and performance enhancements. There’s a significant focus on closing gaps and adding retry strategies for better stability, especially concerning cloud providers. Notably, if Nextflow’s API calls against cloud providers fail for any server-side reason, it will retry automatically, avoiding pipeline failures caused by temporary server issues.

Publishing Changes

Previously, if a file failed to publish, Nextflow would only issue a warning. It was possible for a pipeline to complete successfully without noticing missing output files. Now, by default, Nextflow will fail the pipeline if the publishing fails, though there’s an option to revert to the old behavior. Additionally, retry strategies for publishing have been introduced to ensure retry attempts if an issue arises.

Job Arrays

One highly requested feature is the introduction of job arrays. This allows users to submit many jobs as a single submission, alleviating strain on schedulers. The submission happens in a batch, and then the scheduler can process and plan effectively. Once a job is submitted as part of a job array, the jobs run independently. If any child job fails, it is resubmitted without affecting the rest of the array.

Singularity OCI mode and GA4GH TES

In the past, Singularity supported Docker images by converting them into SIF files, consuming storage and time. Now, both Singularity and Apptainer can run OCI images directly, saving valuable resources.

Additionally, the TES executor has seen significant improvements, now supporting TES 1.1, which brings broader compatibility and integration with existing workflows.

Major new syntax features

Topic Channels

A new feature called topic channels offers a more straightforward approach to collecting channel outputs across pipelines. Channels can emit data to a named topic, simplifying the collection and use of version information from various processes within Nextflow pipelines.

Eval Outputs

Eval outputs simplify the addition of shell commands to tasks. With eval outputs, necessary post-task commands can be defined neatly, avoiding repetitive code within process definitions.

Workflow Output Definition

The concept of workflow output definitions has been introduced. This new syntax streamlines the publication of files by defining publish targets within workflows. Instead of defining publication behaviors within process definitions, users can now manage them at the workflow level, ensuring better clarity and fewer repetitions in the code.

Join us to hear Phil Ewels chat with Maxime Garcia

Tune in to hear all about Pixelgen Technologies - creators of a novel technology

We chat about how this fascinating technology works, what you can do with the data

Links:

Chapters:

Evan Floden (CEO and co-founder of Seqera) joins Phil Ewels (Product Manager for OSS at Seqera) to talk about two of the big announcements at the recent Nextflow Summit Boston 2024 - Seqera Pipelines and Seqera Containers.

00:00 - Introduction

00:37 - Nextflow Summit Boston 2024

01:14 - Summit talks available online

01:57 - Summit announcements

04:32 - Seqera Pipelines - motivations

05:59 - Seqera Pipelines - first look

06:48 - Testing requirements for community pipelines

10:05 - How we tested pipelines

11:53 - SRA-Explorer tangent

12:34 - Seqera Pipelines - live demo

16:14 - Getting Nextflow launch commands

19:12 - Seqera Containers - intro

24:03 - Seqera Containers - live demo

27:13 - Containers - ARM cpu arch builds

28:33 - Singularity containers

29:09 - Wave CLI

31:19 - Nextflow with Seqera Containers

33:22 - Seqera Containers - future usage

35:09 - Where to read more

36:53 - Thank you to the community

Join us as we discuss the brand new @nf-core / EuroFaang pre-print! 🔥 We chat to some of the key authors, covering the background to the paper, the main messages and how EuroFAANG and nf-core have collaborated. 🧬 👩🏻‍🔬