Top 16 nextflow Open-Source Projects

• nextflow

  9 2,551 9.7 Groovy

  A DSL for data-driven computational pipelines

  

Project mention: Nextflow: Data-Driven Computational Pipelines | news.ycombinator.com | 2023-08-10

> 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.

• rnaseq

  14 785 9.4 Nextflow

  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

  

Project mention: R pipelines for bulk RNA-seq analyses | /r/bioinformatics | 2023-12-09

• InfluxDB

  www.influxdata.com featured

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• awesome-nextflow

  2 546 0.0

  A curated list of nextflow based pipelines

  

• sarek

  5 340 9.9 Nextflow

  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

  

• patterns

  1 317 4.5 Nextflow

  A curated collection of Nextflow implementation patterns (by nextflow-io)

  

• npm-groovy-lint

  4 185 8.5 JavaScript

  Lint, format and auto-fix your Groovy / Jenkinsfile / Gradle files using command line

• mag

  2 182 9.4 Nextflow

  Assembly and binning of metagenomes

  

• SaaSHub

  www.saashub.com featured

  SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

  

• chipseq

  1 173 0.0 Nextflow

  ChIP-seq peak-calling, QC and differential analysis pipeline.

  

• atacseq

  2 161 7.0 Nextflow

  ATAC-seq peak-calling and QC analysis pipeline

  

• eager

  1 124 7.6 Nextflow

  A fully reproducible and state-of-the-art ancient DNA analysis pipeline

  

• configs

  1 77 9.7 Nextflow

  Config files used to define parameters specific to compute environments at different Institutions (by nf-core)

  

• vscode-groovy-lint

  1 66 8.0 Groovy

  VSCode extension to lint , correct and format groovy and Jenkinsfile

Project mention: New version of VSCode Groovy Lint refactored | news.ycombinator.com | 2023-12-17

• rnaseq-nf

  1 62 5.5 Nextflow

  A proof of concept of RNAseq pipeline

  

• website

  1 61 9.9 Astro

  Code and files for the main nf-core website. (by nf-core)

  

Project mention: Setting up Doom Emacs for Astro Development | dev.to | 2024-04-23

I've rewritten this website, my partner's website, my university rugby club's website. I'm moving my Applied Genomics course website to Starlight, the Astro team's documentation framework. The nf-core site has been rewritten in Astro and Svelte from PHP. I'm all in.

• hlatyping

  1 52 0.0 Nextflow

  Precision HLA typing from next-generation sequencing data

  

• tronflow-vcf-postprocessing

  1 6 0.0 Shell

  A Nextflow variant normalization pipeline based on vt and bcftools

  

• SaaSHub

  www.saashub.com featured

  SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

  

nextflow related posts

• Point of using Hisat2 build to index reference genomes when working with known genomes mouse/human?

  1 project | /r/bioinformatics | 29 May 2023

• I used featureCounts to quantify RNA-seq reads and got a low successful alignment percentage. Is this a problem?

  1 project | /r/bioinformatics | 18 May 2023

• Recommendations for software or online resources

  1 project | /r/bioinformatics | 29 Apr 2023

• What are some good examples of well-engineered bioinformatics pipelines?

  8 projects | /r/bioinformatics | 5 Apr 2023

• How to know where to align if I have RNAseq data??

  1 project | /r/bioinformatics | 9 Mar 2023

• Pipeline to analyze ATAC seq

  3 projects | /r/bioinformatics | 25 Feb 2023

• Semi Budget-Friendly High-Thread Count Options?

  1 project | /r/HomeServer | 13 Feb 2023
• A note from our sponsor - InfluxDB
  www.influxdata.com | 13 May 2024

  Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality. Learn more →

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