The choice of groovy was unfortunate, but yet it still seems more popular than snakemake which I can only attribute to the nf-core set of curated workflows.
I have a dislike of nextflow because it submits 10s of thousands of separate jobs to our HPC scheduler which causes a number of issues, though they've now added support for array jobs which should hopefully solve that.
samuell · 26m ago
To implement an efficient dataflow-based programming API/DSL, you better have some support for channels and lightweight threads in a scriptable language, something that you've got in Groovy with the GPars library that Nextflow uses.
We opted for implementing all of this in Go in SciPipe, where we get similar basic dataflow/flow-based functionality as Nextflow with the native concurrency primitives of Go, but the Go syntax probably/surely puts away some biologists who have written some python at most before, and Go won't let us customize the API and hide away as much of the plumbing under nice syntax, as Groovy.
In this regard, Groovy with the GPars library for the concurrency, doesn't seem as a particularly bad choice. There weren't that many options at the time either.
The downside has been tooling support though, such as editor intelligence and debugging support, although parts of that is finally improving now with a NF language server.
Today, one could probably implement something similar with Python's asyncio and queues for the channel semantics, and there is even the Crystal language that has Go-like concurrency in a much more script-like language (see a comparison between Go and Crystal concurrency syntax at [1]), but Crystal would of course be an even more fringe langauge than Groovy.
At a previous Biotech, we used Cromwell/WDL because the DSL was the most intuitive to our bioinformatics scientists. But seeing as that doesn't work as nicely on AWS (and is also supported by an organization that is imploding), we opted for Argo on our K8s cluster to process RNAseq data en masse. Getting the scientists to use YAMl has been an uphill struggle, but the same issues would apply to learning groovy I guess. We've found that the Argo engine is easier to maintain, and also we only have to support one orchestrator across our Bioinformatics and ML teams.
For industrial purposes, I've started to approach these pipelines as a special case of feature extraction and so I'm reusing our ML infrastructure as much as possible.
totalperspectiv · 2h ago
I would rather write Groovy than YAML any day of the week.
Why did you rule out Nextflow or Snakemake? I believe they both work with k8 clusters.
Argo doesn’t look great from my standpoint as a workflow author.
totalperspectiv · 5h ago
Cool seeing a workflow language pop up on HN!
Nextflow and Snakemake are the two most-used options in bioinformatics these days, with WDL trailing those two.
I really wish Nextflow was based on Scala and not Groovy, but so it goes.
I've used Snakemake my whole life, can someone experienced with both systems share whether jumping to nextflow is worth it?
Protostome · 1h ago
I have pipelines written in both frameworks.
Nextflow (despite the questionable selection of groovy as the language of choice) is more powerful and enables greater flexibility in terms of information flow.
For example, snakemake makes it very difficult if not impossible to create pipelines that deviate from a DAG architecture. In cases where you need loops, conditionals and so on, Nextflow is a better option.
One thing that I didn't like about nextflow is that all processes can either run under apptainer or docker, you can mix and match docker/apptainer like you do in snakemake rules.
chrisweekly · 33m ago
"you can mix and match"
you meant "CAN'T", right?
totalperspectiv · 2h ago
NF Tower / Seqera would be the selling points. They offer a nice UX for managing pipelines and abstract over AWS.
Technically snakemake can do it all. But in practice NF seems to scale up a bit better.
That said, if you don’t need the UI for scientists, I’d stick to snakemake.
I have a dislike of nextflow because it submits 10s of thousands of separate jobs to our HPC scheduler which causes a number of issues, though they've now added support for array jobs which should hopefully solve that.
We opted for implementing all of this in Go in SciPipe, where we get similar basic dataflow/flow-based functionality as Nextflow with the native concurrency primitives of Go, but the Go syntax probably/surely puts away some biologists who have written some python at most before, and Go won't let us customize the API and hide away as much of the plumbing under nice syntax, as Groovy.
In this regard, Groovy with the GPars library for the concurrency, doesn't seem as a particularly bad choice. There weren't that many options at the time either.
The downside has been tooling support though, such as editor intelligence and debugging support, although parts of that is finally improving now with a NF language server.
Today, one could probably implement something similar with Python's asyncio and queues for the channel semantics, and there is even the Crystal language that has Go-like concurrency in a much more script-like language (see a comparison between Go and Crystal concurrency syntax at [1]), but Crystal would of course be an even more fringe langauge than Groovy.
[1] https://livesys.se/posts/crystal-concurrency-easier-syntax-t...
For industrial purposes, I've started to approach these pipelines as a special case of feature extraction and so I'm reusing our ML infrastructure as much as possible.
Why did you rule out Nextflow or Snakemake? I believe they both work with k8 clusters.
Argo doesn’t look great from my standpoint as a workflow author.
Nextflow and Snakemake are the two most-used options in bioinformatics these days, with WDL trailing those two.
I really wish Nextflow was based on Scala and not Groovy, but so it goes.
There is a Draft up for dsl3 that adds static types to the channels that I’m very excited about. https://github.com/nf-core/fetchngs/pull/309
For example, snakemake makes it very difficult if not impossible to create pipelines that deviate from a DAG architecture. In cases where you need loops, conditionals and so on, Nextflow is a better option.
One thing that I didn't like about nextflow is that all processes can either run under apptainer or docker, you can mix and match docker/apptainer like you do in snakemake rules.
you meant "CAN'T", right?
Technically snakemake can do it all. But in practice NF seems to scale up a bit better.
That said, if you don’t need the UI for scientists, I’d stick to snakemake.