#nextflow 23.09.0 released https://github.com/nextflow-io/nextflow/releases/tag/v23.09.0-edge

2/ but where the other aspects have been tailored to R&D and taken care of. 💰 Simple account and budget control so you can easily and calmly give access to students and new users. Seamless batch processing with workflow managers such as #Nextflow, the ultimate pipeline boost! 🚀

🔍 Curious if there are fellow #Nextflow & #AWS users here yet! 🤔 I have a few of blog posts on my site that might be helpful—especially if you're delving into Nextflow on AWS Batch. 🚀🌟 #Bioinformatics

🌐🔗 https://lpembleton.rbind.io/blog

Is there a clean way to make a Nextflow operator(s) work like zip() in Python, collecting the elements of each item together pairwise? For example for a channel with the items

[1, “One”]
[2, “Two”]
[3, “Three”]

producing a channel with a single item:

[[1, 2, 3], [“One”, “Two”, “Three”]]

#Nextflow

Anyone else notice that ChatGPT isn’t that good at #Nextflow code? Maybe its getting confused and mixing groovy with nextflow syntax.

Love #nextflow ? Love @nf_core? Come and join my team at #seqeralabs as a Developer Advocate / community builder! 👷🤩 Now looking for a new team member to represent North America 🇺🇸🇨🇦
Let's build this community together! 🚀

Remote (ET 🕐🌎)

https://seqera.io/careers/developer-advocate/

#nextflow 23.7.0 released. https://github.com/nextflow-io/nextflow/releases/tag/v23.07.0-edge

If you're in Chicago Aug 10, I'll be giving a talk on building Python-centered workflows to search through terabytes of genomic data, along with #Nextflow and #neo4j
at Chipy
https://www.chipy.org/meetings/230/

Also, workflow engines cannot pick up modules reliably, as module naming schemes may differ from cluster to cluster. Hence, they rely on conda and add options allowing for environment modules and/or containerized software.

The HPC world needs to find an answer, as reproducible workflows carried out by workflow engines such as #snakemake or #nextflow are what data analysis communities are working with (across fields).

The filesystem was blameless. The problem was an extraneous input path (a log file) was being overwritten by a file of the same name. #NextFlow

Nextflow-cache-hash-changed-and-I-don’t-know-why* blues.

https://www.nextflow.io/blog/2022/caching-behavior-analysis.html

*I suspect it might be the scratch filesystem not preserving timestamps, so trying `cache 'lenient` as a first step. #Nextflow

You are doing #Bioinformatics? Would you say data analysis requires interactive work, e.g. using jupyter, rstudio, etc.? Or would you prefer using a workflow system, e.g. #snakemake, #nextflow, #galaxy, etc.?

I am not talking about visualization, though. Visualization is important and can be achieved regardless of the approach.

Please boost. Thank you.

A good indicator is: curated support for workflow engines such as #snakemake, #nextflow, #galaxy .

One of the benefits of using a #pipeline system of #bioinformatics #workflow like #Nextflow, is that it reports the total amount of compute #power that was used, which approximates the amount of #energy consumed. For instance, yesterday I aligned 16 pairs of trypanosome genomes; it took ~20 minutes but consumed ~20 hours of CPU cores. Assuming 10 Watts per core, this makes 200 Wh, which is 720 000 #Joules. One would need to multiply this by some factor to account for cooling the server room etc.

Great article describing all the different file systems supported by @nextflowio (there are a lot!) with practical recommendations as to which are best suited to different setups.. Well worth a read!
---
RT @nextflowio
🔍 Are you looking to optimize the performance of your #Nextflow pipelines? 🚀 Choosing the right storage architecture can make all the difference.

📖 Check out this article for tips to help you make the right decision: htt…
https://twitter.com/nextflowio/status/1654125016420864000

Comprehensive survey of the different storage options out there and how they impact performance when using @nextflowio 👇
---
RT @nextflowio
🔍 Are you looking to optimize the performance of your #Nextflow pipelines? 🚀 Choosing the right storage architecture can make all the difference.

📖 Check out this article for tips to help you make the right decision: http://ow.ly/JgxK50OfN7j

#datastorage #bioinformatics
https://twitter.com/nextflowio/status/1654125016420864000

Nextflow tells us that using `process().set(name)` is more idomatic than `name = process()`.

But is it really? Is this not more confusing and trickier to follow, especially to those used to languages like Python that assign variables in this way?

Would you recommend this style?

https://www.nextflow.io/docs/latest/operator.html#set

#nextflow #bioinformatics

RT @nf_core
🚨Just a reminder that the deadline for applying to the 3rd round of the #Nextflow and #nf_core mentorship closes on May, 1st! 😉 More info at https://nf-co.re/mentorships

In the meantime, read our blog post about the second round that just ended 🤩

https://www.nextflow.io/blog/2023/czi-mentorship-round-2.html

Really nice blog post about the 2nd round of @nextflowio / @nf_core mentorships, with a bunch of testimonials and short project descriptions..

If you're not sure about applying for the 3rd round, have a read! Some great inspiration here! 🎉
---
RT @nf_core
🚨Just a reminder that the deadline for applying to the 3rd round of the #Nextflow and #nf_core mentorship closes on May, 1st! 😉 More info at https://nf-co.re/mentorships

In the meantime…
https://twitter.com/nf_core/status/1648010232931516416

RT @SeqeraLabs
🇬🇧 London alert! We're exhibiting at @PistoiaAlliance Annual Spring Conference on April 18. @ChrisjTownend and @aka_hpatel look forward to meeting the Alliance members and sharing how Seqera enables collaborative data analysis at scale.

#nextflow

https://www.pistoiaalliance.org/eventdetails/pistoia-alliance-annual-spring-conference-2023/