nextflow VS cgpipe

> It's been a while since you can rerun/resume Nextflow pipelines

Yes, you can resume, but you need your whole upstream DAG to be present. Snakemake can rerun a job when only the dependencies of that job are present, which allows to neatly manage the disk usage, or archive an intermediate state of a project and rerun things from there.

> and yes, you can have dry runs in Nextflow

You have stubs, which really isn't the same thing.

> I have no idea what you're referring to with the 'arbitrary limit of 1000 parallel jobs' though

I was referring to this issue: https://github.com/nextflow-io/nextflow/issues/1871. Except, the discussion doesn't give the issue a full justice. Nextflow spans each job in a separate thread, and when it tries to span 1000+ condor jobs it die with a cryptic error message. The option of -Dnxf.pool.type=sync and -Dnxf.pool.maxThreads=N prevents the ability to resume and attempts to rerun the pipeline.

> As for deleting temporary files, there are features that allow you to do a few things related to that, and other features being implemented.

There are some hacks for this - but nothing I would feel safe to integrate into a production tool. They are implementing something - you're right - and it's been the case for several years now, so we'll see.

Snakemake has all that out of the box.

For now, I think that the best place to track this / get your voice heard is this GitHub Discussions post (which covers many things - error reporting is one of them). https://github.com/nextflow-io/nextflow/discussions/3107

We could spend the day pointing to things we wish were different, but that doesn't change the fact that Nextflow is the leader when it comes to workflow orchestration. And feel free to create a new issue in the GitHub repository if you wish to request a feature :)

The nextflow devs have been talking about this for a while on GitHub. Looks like they're implementing something along these lines using schema like they do for nf-core. GitHub discussion.

Groovy definitely scales up just fine I think but I never used it myself outside of little snippets embedded in my DSL, I know its considered by some to be "dead" so its interesting to see what other JVM-ecosystem users think of it.

I do too.. and have similar opinions. I wrote my own tool years back for pipelines because it was always frustrating (started roughly around the same time as Nextflow).

Allowing for files to be marked as transient (temp) and re-running from arbitrary time points are definitely one of the things I support... as is conditional logic within the pipeline for job definition and resource usage. For me though, one of the biggest things is that I like having composable pipelines, so each part of the larger workflow can be developed independently. They can interact with each other (DAG) and use existing dependencies, but they don't have to exist in the same document/script. I work on large WGS datasets, so 1000's of jobs per patient isn't uncommon.

Happy to talk more if you're interested.

https://github.com/compgen-io/cgpipe

(And yes, you can dry run the entire thing. It will write out a bash script if you want to see exactly what is going to run without submitting jobs.)