Learning Nextflow

Question

[AIMAR]

Hello and hope all is well. I would like to know if there is someone among us who can provide me with resources to learn Nextflow apart from what Nf-Core offers.

I'm looking to write my bash scripts in Nextflow in order to run them with Nextflow for fast, reproducible and efficient analysis.

Thanks !

Answer 1

[Raony Guimarães]

Hi there,

Here is a good list of resources you can use:

https://github.com/nextflow-io/awesome-nextflow

[Phil Ewels]

This repo is very dated now (most content is > 3 years old) so I'd be a little cautious of it. I've been wondering if we should archive it for a while now to be honest.

[Marcel Ribeiro-Dantas]

I opened/merged a PR this morning with small updates, but I agree you with XD

[AIMAR]

Thanks very much for the share.

Answer 2

[Maxime Garcia]

I would recommend going directly to the Nextflow training: https://training.nextflow.io/ The hello nextflow series is I think pretty good (but I am slightly biased ;-))

[AIMAR]

Thank you so much sir for this information. I had the opportunity to watch your videos on training sessions in French and it helped me.

However, being a biologist by training who has recently discovered bioinformatics and I'm trying to train myself to be an expert, I'm having some problems understanding the concepts related to coding and programming.

[Marcel Ribeiro-Dantas]

You're referring to an outdated version of the Nextflow official training material. The video you're referring was recorded over 2 years ago. Lots of improvements occurred ever since, and there is a new training material now called "Hello Nextflow" whose expected audience is complete beginners :) You can find it clicking here.

[AIMAR]

it's because in the beginning I could'nt understand the english version so I've found the french one, but thanks for the share and I'll watch them for sure !

[iraun]

If you're transitioning from biology to bioinformatics, in addition to Nextflow traininng, some basic knowledge of Python, R and Bash/Linux would be recommended, which will help your understanding of coding and programming-related problems. Additionally, understanding common bioinformatics analyses, e.g. variant calling, variant annotation, expression quantification, and enrichment analysis, will help your transition. There are many free online resources, like Coursera, that offer a variety of courses on these topics.

[AIMAR]

I'm familiar with Bash/Linux and can understand a few python programs. As far as omics analysis like genomics or transcriptomics ...etc. is concerned.

I understand all these concepts because I studied genomic and NGS technologies during my master's degree.

It's just the transition to bioinfo that requires a very good understanding of logical reasoning to write a program or pipeline in a certain language.

Thanks very much for the help and advices, I appreciate.

Answer 3

[Juke34]

Here the nice ressources I have collected

• Nextflow Training from Fundamentals to Advanced The offical trainings from nextflow.io.
• Nextflow workshop for beginners - by vagkaratzas
• nf-core Training - by Zemzemfiras1
• Software Carpentry Nextflow training. High quality course made by the Software Carpentry.
• nextflow-training - by Aubin THOMAS IGH Montpellier

[AIMAR]

Thanks for the share I appreciate .