Nextflow Pipeline

Open-source Nextflow projects categorized as Pipeline

Top 7 Nextflow Pipeline 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? | | 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? | | 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 | | 2022-11-30

    Launching [pensive_euler] DSL2 - revision: 51eba00b32 [master]

  • atacseq

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

    Project mention: Software repository and hackathons | | 2022-06-29
  • mag

    Assembly and binning of metagenomes

    Project mention: How do you use 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

  • SonarLint

    Clean code begins in your IDE with SonarLint. Up your coding game and discover issues early. SonarLint is a free plugin that helps you find & fix bugs and security issues from the moment you start writing code. Install from your favorite IDE marketplace today.

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 Pipeline related posts


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

Project Stars
1 rnaseq 561
2 sarek 224
3 chipseq 137
4 atacseq 128
5 mag 112
6 eager 85
7 hlatyping 37
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