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Top 7 Nextflow Workflow Projects
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rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
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.
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sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
The sarek pipeline from nf-core might interest you
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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.
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Launching https://github.com/nf-core/chipseq [pensive_euler] DSL2 - revision: 51eba00b32 [master]
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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.
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SonarQube
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Nextflow Workflow related posts
- How to get NGS programming experience?
- Illumina: can I use it on my laptop?
- What is the preferred way of documenting a Nextflow pipeline?
- Software repository and hackathons
- GATK4 automated pipelines in existence?
- Introduction to RNAseq and microRNA?
- Workflow Question
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A note from our sponsor - InfluxDB
www.influxdata.com | 8 Feb 2023
Index
What are some of the best open-source Workflow projects in Nextflow? This list will help you:
Project | Stars | |
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1 | rnaseq | 561 |
2 | sarek | 225 |
3 | chipseq | 138 |
4 | atacseq | 129 |
5 | mag | 114 |
6 | eager | 86 |
7 | hlatyping | 38 |