39 episodes

Nextflow is a leading open-source workflow orchestrator that simplifies writing and deploying compute and data-intensive pipelines at scale on any infrastructure. In this podcast we discuss news in the Nextflow ecosystem and speak with pioneers in the field.

Channels - the nextflow podcast Seqera

    • Science

Nextflow is a leading open-source workflow orchestrator that simplifies writing and deploying compute and data-intensive pipelines at scale on any infrastructure. In this podcast we discuss news in the Nextflow ecosystem and speak with pioneers in the field.

    Episode 39: Spatial proteomics at Pixelgen

    Episode 39: Spatial proteomics at Pixelgen

    Tune in to hear all about Pixelgen Technologies - creators of a novel technology
    for doing single-cell spatial proteomics.



    We chat about how this fascinating technology works, what you can do with the data
    and why they chose to develop their analysis suite as an open-source nf-core pipeline.



    Links:


    Software:

    nf-core/pixelator pipeline
    Pixelator Python package


    Science:

    Nature Methods publication: “Molecular pixelation: spatial proteomics of single cells by sequencing”


    Presentations:

    Nextflow Summit 2022 talk: “Pixelgen Technologies ❤︎ Nextflow”
    Nextflow Summit 2024 Boston talk: “Nextflow allows Pixelgen innovation engine to reach the market quicker”
    Nextflow Summit 2024 Barcelona


    Pixelgen:

    Pixelgen Technologies homepage
    @PixelgenTech on twitter / X and LinkedIn


    BioLizard:

    BioLizard homepage
    @BioLizard_nv on twitter / X and LinkedIn





    Chapters:


    Start (00:00)
    Welcome (00:09)
    Introductions (00:50)
    Intro to Pixelgen Technologies (01:41)
    Lab methods (03:08)
    Nature Methods publication (06:15)
    Data visualisation (09:35)
    Working with single cell data (12:29)
    Cell interactions (15:06)
    Why Pixelgen chose open source (16:05)
    Pixelator Python package (20:10)
    Building within nf-core (21:40)
    Florian - Biolizard (23:01)
    Pipeline overview (25:19)
    Using nf-core from a commercial setting (26:50)
    Coming out of stealth (28:53)
    Extending Pixelator (32:24)
    Dealing with customers (34:58)
    Looking to the future (39:38)
    Interactive analysis (41:32)
    Advice for others (43:12)
    Pixelgen at the Nextflow Summit (45:16)

    • 46 min
    Episode 38: Seqera Pipelines & Seqera Containers

    Episode 38: Seqera Pipelines & Seqera Containers

    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.

    We dive into what these two new community offerings are, why we built them and how they work.

    Links:


    https://seqera.io/pipelines/
    https://seqera.io/containers/
    Announcement blog post
    Nextflow Summit Boston 2024 agenda
    Summit YouTube playlist
    Nextflow 24.04 blog post



    Timeline:

    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

    • 37 min
    Episode 37: The nf-core / EuroFAANG pre-print

    Episode 37: The nf-core / EuroFAANG pre-print

    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. 🧬 👩🏻‍🔬

    • 54 min
    Episode 36: The Nextflow Ambassadors Program

    Episode 36: The Nextflow Ambassadors Program

    Join us in this episode of the Channels podcast for a closer look at the Nextflow Ambassadors Program. Marcel Ribeiro-Dantas and Geraldine Van der Auwera discuss the origins of the program, recent highlights and next steps, including the open call for new Ambassadors, which will close June 14.

    Relevant links:


    Call for applications: https://www.nextflow.io/ambassadors.html
    Original announcement: https://www.nextflow.io/blog/2023/introducing-nextflow-ambassador-program.html
    Marcel’s favorite Ambassador-contributed Nextflow blog post: https://www.nextflow.io/blog/2024/reflections-on-nextflow-mentorship.html

    • 24 min
    Episode 35: Nextflow plugins - A plugin development walkthrough

    Episode 35: Nextflow plugins - A plugin development walkthrough

    This podcast episode is quite different to normal. Rather than an interview or a discussion, you'll get to watch as Ben Sherman guides Phil Ewels through the process of creating a new Nextflow Plugin from scratch. Right from the first line of code to creating a release and publishing the plugin.

    Nextflow plugins have been getting more attention lately and we've been getting a lot of questions in the community. There is better documentation and resources planned, but in the mean time we hope that this can be a useful guide for anyone curious in how they work, and interested in getting started.

    After this we will be back to our usual routine in the podcast, but we'd love to hear what you thought of this taster!




    00:00:00 Welcome
    00:03:27 Nextflow docs
    00:08:34 Starting by forking nf-hello
    00:10:32 Overview of project files
    00:17:13 Trying a first compile
    00:18:12 Different publishing methods
    00:19:54 nf-boost local publish method
    00:23:05 Trying the new compile
    00:24:00 Running locally with the plugin
    00:27:32 Looking at the nf-hello plugin code
    00:39:29 Deleting files we don't need
    00:42:34 Finding event names in the Nextflow source
    00:47:46 Writing some custom functions
    00:49:41 Testing our new code
    00:51:51 Modifying the test pipeline to create files
    00:54:14 Coding up the JSON output
    00:59:20 Looking at nf-prov code for BCO files
    01:05:30 Testing JSON output
    01:09:39 Automatic work dir cleanup / nf-boost
    01:12:17 Publishing a release on GitHub
    01:19:07 Custom plugin repositories
    01:26:47 Publishing for all Nextflow users
    01:29:52 Conclusion and end

    • 1 hr 32 min
    Episode 34: Nextflow in materials science with Jakob Zeitler

    Episode 34: Nextflow in materials science with Jakob Zeitler

    In this episode of Channels, we talk to Jakob Zeitler - Head of R&D at Matterhorn Studios.

    We dive into how they use Nextflow and Seqera Platform for material science research, paving the way for cheaper and more eco-friendly products for the future ⚗️👩🏻‍🔬🔬🌎

    It may not be bioinformatics, but there's a lot that's in common!

    • 1 hr

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