Top 7 Nextflow Pipeline Projects

rnaseq

7 561 8.6 Nextflow

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

1 224 9.9 Nextflow

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

www.influxdata.com
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chipseq

1 137 10.0 Nextflow

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

1 128 0.0 Nextflow

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

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

1 112 9.1 Nextflow

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

0 85 8.9 Nextflow

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

0 37 0.0 Nextflow

Precision HLA typing from next-generation sequencing data
SonarLint

www.sonarlint.org
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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.