Displaying 1 to 20 from 28 results

nextflow - A DSL for data-driven computational pipelines

  •    Groovy

With the rise of big data, techniques to analyse and run experiments on large datasets are increasingly necessary. Parallelization and distributed computing are the best ways to tackle this kind of problem, but the tools commonly available to the bioinformatics community traditionally lack good support for these techniques, or provide a model that fits badly with the specific requirements in the bioinformatics domain and, most of the time, require the knowledge of complex tools or low-level APIs.

Sarek - Detect germline or somatic variants from normal or tumour/normal whole-genome sequencing data

  •    Nextflow

Previously known as the Cancer Analysis Workflow (CAW), Sarek is a workflow tool designed to run analyses on WGS data from regular samples or tumour / normal pairs, including relapse samples if required. It's built using Nextflow, a bioinformatics domain specific language for workflow building. Software dependencies are handled using Docker or Singularity - container technologies that provide excellent reproducibility and ease of use. Singularity has been designed specifically for high-performance computing environments. This means that although Sarek has been primarily designed for use with the Swedish UPPMAX HPC systems, it should be able to run on any system that supports these two tools.

companion - Pipeline for automatic eukaryotic parasite annotation

  •    Lua

A portable, scalable eukaryotic genome annotation pipeline implemented in Nextflow. It supports parallelized execution on a single machine as well as on large cluster platforms (LSF, SGE, ...).

awesome-nextflow - A curated list of nextflow based pipelines

  •    

A curated list of Nextflow pipelines inspired by other awesome-* lists.




crg-course-nov16 - Nextflow + Docker tutorial material

  •    

This repository contains the tutorial material for the Parallel distributed computational workflows with Nextflow and Docker containers course. The second example adds the buildIndex process. It takes the genome file as input and creates the genome index by using the bowtie-build tool.

hack17-tutorial - Nextflow basic tutorial for newbie users

  •    Nextflow

This repository contains the tutorial material for the Nextflow workshop.

nf-hack17 - Nextflow hackathon 2017 projects

  •    Shell

This repository lists the project ideas and the material used during the hackathon organised in the context of the Nextflow workshop that will take on 14-15 September 2017 in Barcelona. PRBB building, Charles Darwin room, ground floor (you will need an ID card to enter in the building).

patterns - A curated collections of Nextflow implementation patterns

  •    Nextflow

A curated collections of Nextflow implementation patterns


rnaseq-nf - A proof of concept of RNAseq pipeline

  •    Nextflow

A basic pipeline for quantification of genomic features from short read data implemented with Nextflow. If you don't have it already install Docker in your computer. Read more here.

rnatoy - A proof of concept RNA-Seq pipeline with Nextflow

  •    Nextflow

A proof of concept of a RNA-Seq pipeline intended to show Nextflow scripting and reproducibility capabilities.

nextflow-demos - Example Nextflow pipelines and programming techniques

  •    Nextflow

Demonstrations of various programming techniques for use inside Nextflow pipelines. This repository is meant to be a supplement to the official Nextflow documentation (links below). Each subdirectory contains files to run sample Nextflow pipelines.

IARC-nf - List of IARC bioinformatics nextflow pipelines

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Install java JRE if you don't already have it (7 or higher). Install nextflow.

needlestack - Multi-sample somatic variant caller

  •    R

Warning: development in progress, unreliable results warranted. Please wait upcoming publication before using it in production.

RNAseq-nf - RNAseq analysis pipeline

  •    HTML

Nextflow : for common installation procedures see the IARC-nf repository.

nanoflow - :microscope: De novo assembly of nanopore reads using nextflow

  •    Nextflow

Nanoflow aims at being a reproducible pipeline for bacterial genome assembly of nanopore reads. You'll also need docker installed if you wish to run the pipeline locally.

docker-benchmarks - A benchmarks of genomic pipelines running in Docker containers

  •    HTML

(if you don't want or cannot use Docker, you will need to download and install the required dependencies: R, Datamash, Make and Groovy. See the included Dockefile for configuration details). Each of these folders contains a Makefile and other scripts used by it to generate the figures. Raw data of each executions are the files docker_{1..10}/trace.csv and native_{1..10}/trace.csv in the same folder.

kallisto-nf - A nextflow implementation of Kallisto & Sleuth RNA-Seq Tools

  •    Nextflow

Make sure you have all the required dependencies listed in the last section. By default the pipeline is executed against the provided example dataset. Check the Pipeline parameters section below to see how enter your data on the program command line.

piper-nf - RNA mapping pipeline

  •    Nextflow

Make sure you have all the required dependencies listed in the last section. By default the pipeline is executed against the provided example dataset. Check the Pipeline parameters section below to see how specify your input data on the program command line.

grape-nf - An automated RNA-seq pipeline using Nextflow

  •    Shell

Grape provides an extensive pipeline for RNA-Seq analyses. It allows the creation of an automated and integrated workflow to manage and analyse RNA-Seq data. It uses Nextflow as the execution backend. Please check Nextflow documentation for more information.