Nextflow Training Week is a quarterly self-paced online training designed for accessibility and flexibility. Featuring on-demand walkthrough videos (Hello Nextflow only) and support via office hours and the community forum, this event replaces fixed-schedule Community Trainings—allowing learners to start anytime during the week and get timely help from our staff and the global Nextflow community.
This third edition will run Sep 22-26, 2025 and is tailored for newcomers looking to get started with Nextflow.
Throughout the week, participants will work through one of the courses on the Nextflow training portal. The course uses GitHub Codespaces as a free, ready-to-use training environment, eliminating the need for software installation and configuration—only a web browser and a GitHub account are required.
Learn at your own pace: Instructor-led videos will be available on YouTube, guiding you through key Nextflow concepts.
Work as a group: We encourage teams, labs, and local groups to work through the course together virtually or in person.
Get live support: Our staff and Nextflow Ambassadors across multiple time zones will be available to answer questions in the community forum and on Zoom office hours.
Certificate opportunity: Register and complete the end-of-week Nextflow quiz to earn your official completion certificate and demonstrate your newly acquired workflow management skills.
Hi! I’ll be starting the Nextflow Free Online Training on 22nd September. In you last point you mentioned about completing an end-of-week quiz. Where can I find that quiz?
Hi, it can take a few minutes but not more than that. You can try refreshing the page and see if that helps. If that still doesn’t work, please post a screenshot of what you see and we’ll try to get you through this.
You might want to try connecting through a different network. In my experience, I’ve occasionally been unable to access Codespaces on my work network, but switching to a personal network resolved the issue.
I have finished the genomics training set. Will the quiz include questions from this or the first few training sets like hello-nextflow/hello-nf-core? Will the certificate dilineate which training was completed?
What is the difference between naming each module’s nextflow script as main.nf and then importing vs giving each module its own name? In the genomics module, eventually each module was segregated into its own folder with each script named “main.nf”. However, in rnaseq module I see that each file is named after the process itself (eg. fastqc.nf). Are both conventions equally used?2)
In rnaseq module while the reads are read in using a channel “read_ch = channel.fromPath(params.reads)”, the index file is being simply provided as file “HISAT2_ALIGN(TRIM_GALORE.out.trimmed_reads, file (params.hisat2_index_zip))”. Could you help me understand why both are not read in using Channel?
Under rnaseq/data, I don’t find the index file for the genome. Can I download it from somewhere else?
I would like to kindly ask for how long they will remain accessible for participants to use. This would help me plan my follow-up learning and application of the tools covered.
Thank you very much for your support and for organizing such an excellent training.
Hi! We only have a quiz for Hello Nextflow; we plan to add others for our next training week in November.
Everyone is welcome to take the Hello Nextflow quiz even if you did a different course, since Hello Nextflow covers the basics that everyone should know by the time they get to other courses.
Functionally, there is no difference. For nf-core, the standard is to have each process in its own directory with the process definition in main.nf. In this case, the file name can be omitted when importing.
When you provide Groovy values (i.e. a file object in this case) instead of channels as input for a process, Nextflow will automatically convert them to a value channel. In this case, using
would be fully equivalent. Important is the distinction between value and queue channels. The trimmed_reads channel most likely contains multiple entries which should run in separate tasks which are all using the same index file. Using a queue channel for the index file would mean that it would be consumed by the first entry of trimmed_reads causing the process to run only once. So using Channel.fromPath(params.hisat2_index_zip) would not work, as this produces a queue channel. You would need to convert it to a value channel first with e.g. Channel.fromPath(params.hisat2_index_zip).first()
Nextflow Training Week is a quarterly self-paced online training designed for accessibility and flexibility. Featuring on-demand walkthrough videos (Hello Nextflow only) and support via office hours and the community forum, this event replaces fixed-schedule Community Trainings—allowing learners to start anytime during the week and get timely help from our staff and the global Nextflow community.
Are you ready to learn Nextflow? Register now