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evanfloden authored Jun 24, 2019
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# Nextflow training for Phd course 2018
# Nextflow training for the Bioinformatics Summer School 2019

## Nextflow in a nutshell

A workflow engine for data analysis pipelines with a string focus on:
A workflow engine for data analysis pipelines with a strong focus on enabling:
* Portability
* Reproducibility
* Scalability
* Usability

How?
### How?
* Functional/reactive programming model
* Decoupling and tasks isolation
* Concise DSL for recurrent task operations
* Pragmatic, allows quick prototyping and iterations
* Decoupling and isolating tasks
* Concise domain specific language for recurrent task operations
* Pragmatic, allowing quick prototyping and iterations
* Hide complexity
* Coexists with errors (!)

## Prerequisite
### Prerequisite

* Unix-like OS (Linux, macOS, etc.)
* [Java](http://jdk.java.net/) 8 or later
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Then, clone this repository with the following command:

```
git clone https://github.com/cbcrg/nf-phdcourse18 && cd nf-phdcourse18
git clone https://github.com/cbcrg/nf-summerschool && cd cbcrg/nf-summerschool
```

Finally pull the following Docker container:
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## Nextflow hands-on

During this tutorial you will implement a proof of concept of a RNA-Seq pipeline which:
During this tutorial you will implement a proof of concept of a RNA-seq pipeline which:

1. Indexes a trascriptome file.
2. Performs quality controls
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