Share Nextflow pipelines with Github
The GitHub code repository and collaboration platform is widely used between researchers to publish their work and to collaborate on projects source code. Even more interestingly a few months ago...
View ArticleReproducibility in Science - Nextflow meets Docker
The scientific world nowadays operates on the basis of published articles. These are used to report novel discoveries to the rest of the scientific community. But have you ever wondered what a...
View ArticleUsing Docker for scientific data analysis in an HPC cluster
Scientific data analysis pipelines are rarely composed by a single piece of software. In a real world scenario, computational pipelines are made up of multiple stages, each of which can execute many...
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Introducing Nextflow REPL Console
The latest version of Nextflow introduces a new console graphical interface. The Nextflow console is a REPL (read-eval-print loop) environment that allows one to quickly test part of a script or pieces...
View ArticleInnovation In Science - The story behind Nextflow
Innovation can be viewed as the application of solutions that meet new requirements or existing market needs. Academia has traditionally been the driving force of innovation. Scientific ideas have...
View ArticleThe impact of Docker containers on the performance of genomic pipelines
In a recent publication we assessed the impact of Docker containers technology on the performance of bioinformatic tools and data analysis workflows. We benchmarked three different data analyses: a RNA...
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MPI-like distributed execution with Nextflow
The main goal of Nextflow is to make workflows portable across different computing platforms taking advantage of the parallelisation features provided by the underlying system without having to...
View ArticleDeveloping a bioinformatics pipeline across multiple environments
As a new bioinformatics student with little formal computer science training, there are few things that scare me more than PhD committee meetings and having to run my code in a completely different...
View ArticleError recovery and automatic resource management with Nextflow
Recently a new feature has been added to Nextflow that allows failing jobs to be rescheduled, automatically increasing the amount of computational resources requested. The problemNextflow provides a...
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Workflows & publishing: best practice for reproducibility
Publication time acts as a snapshot for scientific work. Whether a project is ongoing or not, work which was performed months ago must be described, new software documented, data collated and figures...
View ArticleDocker for dunces & Nextflow for nunces
Below is a step-by-step guide for creating Docker images for use with Nextflow pipelines. This post was inspired by recent experiences and written with the hope that it may encourage others to join in...
View ArticleDeploy your computational pipelines in the cloud at the snap-of-a-finger
Learn how to deploy and run a computational pipeline in the Amazon AWS cloud with ease thanks to Nextflow and Docker containersNextflow is a framework that simplifies the writing of parallel and...
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Enabling elastic computing with Nextflow
Learn how to deploy an elastic computing cluster in the AWS cloud with Nextflow In the previous post I introduced the new cloud native support for AWS provided by Nextflow. It allows the creation of a...
View ArticleMore fun with containers in HPC
Nextflow was one of the first workflow framework to provide built-in support for Docker containers. A couple of years ago we also started to experiment with the deployment of containerised...
View ArticleNextflow published in Nature Biotechnology
We are excited to announce the publication of our work Nextflow enables reproducible computational workflows in Nature Biotechnology.The article provides a description of the fundamental components and...
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Nextflow workshop is coming!
We are excited to announce the first Nextflow workshop that will take place at the Barcelona Biomedical Research Park building (PRBB) on 14-15th September 2017. This event is open to everybody who is...
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Nextflow and the Common Workflow Language
The Common Workflow Language (CWL) is a specification for defining workflows in a declarative manner. It has been implemented to varying degrees by different software packages. Nextflow and CWL share a...
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Nexflow Hackathon 2017
Last week saw the inaugural Nextflow meeting organised at the Centre for Genomic Regulation (CRG) in Barcelona. The event combined talks, demos, a tutorial/workshop for beginners as well as two...
View ArticleScaling with AWS Batch
The latest Nextflow release (0.26.0) includes built-in support for AWS Batch, a managed computing service that allows the execution of containerised workloads over the Amazon EC2 Container Service...
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Running CAW with Singularity and Nextflow
This is a guest post authored by Maxime Garcia from the Science for Life Laboratory in Sweden. Max describes how they deploy complex cancer data analysis pipelines by using Nextflow and Singularity. We...
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