nextflow | adoptium | |
---|---|---|
9 | 150 | |
2,551 | 173 | |
1.4% | 0.6% | |
9.7 | 6.7 | |
7 days ago | 28 days ago | |
Groovy | ||
Apache License 2.0 | - |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
nextflow
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Nextflow: Data-Driven Computational Pipelines
> 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.
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Alternatives to nextflow?
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
- HyperQueue: ergonomic HPC task executor written in Rust
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Nextflow vs Snakemake
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 :)
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Feel very hard writing nextflow pipeline.
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.
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Need a statically typed Python replacement
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.
adoptium
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How can I implement a simple asynchronous DRAM controller? (2018)
Used the recommended JRT https://adoptium.net/
Wandered through the https://github.com/hneemann/Digital site and saw past issues with JRT but no obvious solution.
I have a couple hundred GALs of same or similar model number of new old stock
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I REALLY NEED HELP WITH THIS SERVER, HUGE ISSUE PLZ
Oracle Java is shit use https://adoptium.net/ or another one
- ClickHouse Keeper: A ZooKeeper alternative written in C++
- OpenTF Renames Itself to OpenTofu
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JDK 21 Release Notes
Some options for those who prefer to avoid the Oracle minefield:
https://adoptium.net
https://aws.amazon.com/corretto
https://www.azul.com/downloads
https://bell-sw.com/pages/downloads
Sadly, no-one has managed to package it yet, but we should get something in the next couple of days. Since 21 is an "LTS" release, major Linux distributions will provide a runtime pretty soon. Ubuntu backports them to old releases too.
- Any JavaFX+Linux user here?
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Downloading Java... couldn't find what I needed when searching the subreddit
https://adoptium.net/ This link?
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Please help!!!! (MultiMc problem)
I'm using this one on MultiMC. https://adoptium.net/
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Help how 2 do this
some of these will take care of java for you, others are more manual. if you need java, I recommend https://adoptium.net/
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Few general questions from hopefully Java beginner-to-be?
You can totally use VSCode. It's Java support is quite good (it really uses Eclipse under the hood basically). You can compile Java code by hand if you install the Java Development Kit. You can also use a build tool to help you. Maven is the most used one. It has a bit of a learning curve but makes using libraries a lot easier.
What are some alternatives?
galaxy - Data intensive science for everyone.
ATLauncher - ATLauncher is a Launcher for Minecraft which integrates multiple different ModPacks to allow you to download and install ModPacks easily and quickly.
argo - Workflow Engine for Kubernetes
docker-images - Official source of container configurations, images, and examples for Oracle products and projects
ploomber - The fastest ⚡️ way to build data pipelines. Develop iteratively, deploy anywhere. ☁️
corretto-17 - Amazon Corretto 17 is a no-cost, multi-platform, production-ready distribution of OpenJDK 17
singularity - Singularity has been renamed to Apptainer as part of us moving the project to the Linux Foundation. This repo has been persisted as a snapshot right before the changes.
javafx-gradle-plugin - Gradle plugin that makes it easy to work with JavaFX 11+
Airflow - Apache Airflow - A platform to programmatically author, schedule, and monitor workflows
adoptium.net - Development of the website has moved to https://github.com/adoptium/website-v2
devops-resources - DevOps resources - Linux, Jenkins, AWS, SRE, Prometheus, Docker, Python, Ansible, Git, Kubernetes, Terraform, OpenStack, SQL, NoSQL, Azure, GCP
SDKMan - The SDKMAN! Command Line Interface