Nextflow Workflow

Open-source Nextflow projects categorized as Workflow

Top 7 Nextflow Workflow Projects

  • rnaseq

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

    Project mention: How to get NGS programming experience? | reddit.com/r/bioinformatics | 2023-01-31

    I would suggest the nf-core/rnaseq pipeline. It's used by many core facilities around the world. Also, there are many more pipelines from nf-core, e.g. Sarek for variant calling.

  • sarek

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

    Project mention: GATK4 automated pipelines in existence? | reddit.com/r/bioinformatics | 2022-03-11

    The sarek pipeline from nf-core might interest you

  • InfluxDB

    Build time-series-based applications quickly and at scale.. InfluxDB is the Time Series Platform where developers build real-time applications for analytics, IoT and cloud-native services. Easy to start, it is available in the cloud or on-premises.

  • chipseq

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

    Project mention: Nextflow issue | reddit.com/r/bioinformatics | 2022-11-30

    Launching https://github.com/nf-core/chipseq [pensive_euler] DSL2 - revision: 51eba00b32 [master]

  • atacseq

    ATAC-seq peak-calling, QC and differential analysis pipeline

    Project mention: Software repository and hackathons | reddit.com/r/longevity | 2022-06-29
  • mag

    Assembly and binning of metagenomes

    Project mention: How do you use Termux? | reddit.com/r/termux | 2022-07-16

    So, I'm a bioinformatician, and currently I am extending my company's data processing pipeline which takes metagenomic sequencing data and performs a number of downstream analyses on it, the results of which are then provided to our customers. Here is an example of such a data processing pipeline: it's a script which orchestrates the execution of a number of tools to get the desired end result. Each of the green bubbles in the flowchart represents a single program which needs to be called specific settings and with data provided to it either by me (as the pipeline input) or from outputs of previous steps in the pipeline.

  • eager

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

  • hlatyping

    Precision HLA typing from next-generation sequencing data

  • SonarQube

    Static code analysis for 29 languages.. Your projects are multi-language. So is SonarQube analysis. Find Bugs, Vulnerabilities, Security Hotspots, and Code Smells so you can release quality code every time. Get started analyzing your projects today for free.

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020). The latest post mention was on 2023-01-31.

Nextflow Workflow related posts

Index

What are some of the best open-source Workflow projects in Nextflow? This list will help you:

Project Stars
1 rnaseq 561
2 sarek 225
3 chipseq 138
4 atacseq 129
5 mag 114
6 eager 86
7 hlatyping 38
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