Nextflow is indeed the best option today. It's sad that it's based on Groovy though, which seems past its heyday as a language/community.

I'm very excited that this is based on Scheme -- I've long wanted a lispy workflow language!

I'm a little concerned about the coverage of the Guix package manager though. I guess instead of writing Dockerfiles the user would have to learn to write Guix packages.

The "Getting Started" example uses samtools so I guess this is oriented towards a similar bioinformatics audience. However without HPC/Cloud support it's probably not too practical, yet.

Addendum: Listened to the FOSDEM 2019 talk, seems like it does support Docker and HPC. However I need AWS Batch support for it to be really useful to me, hopefully that will be implemented at some point.

If there is Docker/HPC/AWS support in the system through its local commands, there will be support.. Check the cluster mode setup in guix documentation (https://www.gnu.org/software/guix/manual/en/guix.html)

Edit: adding gnu guix manual link

> s sad that it's based on Groovy though

It's actually very cool since you can drop in any Java library you like, which is particularly nice in the bioinformatics space where HTSJDK, Picard and co. give you enormous power in that space.

Nextflow does not capture the software required, which is important for reproducibility. Containers are not a solution for this as it only shifts the problem up a level.

My efforts with BioNix (https://github.com/PapenfussLab/bionix) achieve reproducible pipelines by using Nix to capture the software, workflow, and handle execution either locally, on a compute cluster, or HPC.

Guixwl looks similar to BioNix, though BioNix is a thin layer of Nix expressions and Guixwl seems to be more then that and could be more general. BioNix is targeted at bioinformatics and just builds on nixpkgs.

I've been migrating to nextflow over the last month. It really is fantastic. I even use it in place of bash scripts for little things now just because resume is so nice.

It seems to be used mainly for generic operations (locally available in localhost). However, commands like 'sbatch' (HPC manager system) could theoretically be used to manage the infrastructure.. however, again, I dunno if there would have an integration of such commands natively with guix, though it would be interesting..

I'm not sure if you're talking about nextflow, but it has support for many different job managers (slurm plus like ten more), AWS batch, and Google cloud pipelines.

No, I was indeed talking about guix.