nextflow.io

Nextflow - A DSL for parallel and scalable computational pipelines

Nextflow is a fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. You can use your favourite programming language. And tools, exploiting your current skills. Just download and play with it. No installation is required. Are you a Python geek or a PERL hacker? You can start fast with it. Lightweight processes with message passing, no shared memory. Develop on your laptop, run in the grid or scale-out in the cloud with no changes.

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Nextflow - A DSL for parallel and scalable computational pipelines | nextflow.io Reviews

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Nextflow is a fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. You can use your favourite programming language. And tools, exploiting your current skills. Just download and play with it. No installation is required. Are you a Python geek or a PERL hacker? You can start fast with it. Lightweight processes with message passing, no shared memory. Develop on your laptop, run in the grid or scale-out in the cloud with no changes.

<META> KEYWORDS

1 dataflow

2 data-flow

3 dataflow programming model

4 flow-based programming

5 pipeline

6 computational pipeline

7 bioinformatics

8 bioinformatics pipeline

9 RNAseq

10 next gen sequencing

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features,quick start,examples,basic pipeline,mixing scripting languages,blast pipeline,rna seq pipeline,more examples,documentation,blog,about us,nextflow,data driven computational pipelines,find out more,zero config,polyglot,concurrency,scale easily

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Nextflow - A DSL for parallel and scalable computational pipelines | nextflow.io Reviews

https://nextflow.io

Nextflow is a fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. You can use your favourite programming language. And tools, exploiting your current skills. Just download and play with it. No installation is required. Are you a Python geek or a PERL hacker? You can start fast with it. Lightweight processes with message passing, no shared memory. Develop on your laptop, run in the grid or scale-out in the cloud with no changes.

INTERNAL PAGES

nextflow.io

1

Nextflow - Basic pipeline

http://www.nextflow.io/example1.html

This example shows how write a pipeline made up of two simple BASH processes, so that the results produced by the first are consumed by the second process. Line 1: The script starts with a shebang declaration. This allows you to launch your pipeline, as any other BASH script. Line 3: Declares a pipeline parameter named. That is initialized with the value. This value can be overridden when launching the pipeline, by simply adding the option. To the script command line. Line 29: Defines the process input f...

2

Nextflow - Mixing scripting languages

http://www.nextflow.io/example2.html

When using Nextflow your are not limited to BASH scripts, in a pipeline script you can mix any scripting language. In means that for each process. You are free to use the one that fits better its specific task or simply choose the scripting language you prefer. In the above example it is defined a simple pipeline made up of two processes. The first one executes a Perl code, because the script block definition starts with a PERL.

3

Nextflow - About Us

http://www.nextflow.io/about-us.html

Paolo Di Tommaso,. Nextflow is developed by the Comparative Bioinformatics group. At the Barcelona Center for Genomic Regulation (CRG). It is open source software distributed under the GPL3 licence.

4

Nextflow - RNA-Seq pipeline

http://www.nextflow.io/example4.html

The example below shows how put together a RNAseq pipeline with basic functionality. It maps a collection of read-pairs to a given reference genome and outputs the respective transcript model. Try it in your computer. In order to run this pipeline in your computer you will required:. Java 7 (or higher). Install Nextflow entering the following command in the shell terminal:. Curl -fsSL get.nextflow.io bash. Then launch the pipeline execution using this command:. Nextflow run rnatoy -with-docker.

5

Nextflow - Using Docker for scientific data analysis in an HPC cluster

http://www.nextflow.io/blog/2014/using-docker-in-hpc-cluster.html

Using 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 different scripts, system commands and external tools deployed in a hosting computing environment, usually an HPC cluster. For this reason I wanted to test the capabilities of Docker to solve these problems in the cluster available in our institute.

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fidzu.com

Debian

http://www.fidzu.com/fidzu/debian

Francois Marier: Debugging gnome-session problems on Ubuntu 14.04. After upgrading an Ubuntu 14.04 ("trusty") machine to the latest 16.04 Hardware Enablement. Packages, I ran into login problems. I could log into my user account and see the GNOME desktop for a split second before getting thrown back into the LightDM login manager. The solution I found was to install this missing package:. Looking for clues in the logs. The first place I looked was the log file for the login manager (. Script for ibus sta...

smallchangebio.wordpress.com

Notes: Bio in Docker Symposium 2015 day 1: ngs pipelines, workflow tools, volume management | Small Change Bioinformatics

https://smallchangebio.wordpress.com/2015/11/09/bioindocker2015-day1

Notes: Bioinformatics Open Source Conference 2015 day 2 afternoon: Translational, Visualization and Lightning Talks. Notes: Bio in Docker Symposium 2015 day 2: Docker infrastructure and hackathon →. November 9, 2015. Notes: Bio in Docker Symposium 2015 day 1: ngs pipelines, workflow tools, volume management. I’m at the Bio in Docker Symposium. At the Wellcome Collection. In London. This is a great 2 day set of talks and coding sessions around the use of Docker containerization. Which the community can it...

smallchangebio.wordpress.com

Notes: Bioinformatics Open Source Conference 2015 day 2 morning — Ewan Birney, Open Science and Reproducibility | Small Change Bioinformatics

https://smallchangebio.wordpress.com/2015/07/11/notes-bioinformatics-open-source-conference-2015-day-2-morning-ewan-birney-open-science-and-reproducibility

Notes: Bioinformatics Open Source Conference 2015 day 1 afternoon — Standards, Interoperability and Diversity Panel. Notes: Bioinformatics Open Source Conference 2015 day 2 afternoon: Translational, Visualization and Lightning Talks →. July 11, 2015. Notes: Bioinformatics Open Source Conference 2015 day 2 morning — Ewan Birney, Open Science and Reproducibility. I’m at the 2015 Bioinformatics Open Source Conference (BOSC). My other notes from the conference:. Holly Bik and Data Science. Ewan starts by rem...

sangerinstitute.blog

Companion: a new tool to generate and visualize annotation of parasite genomes | Wellcome Trust Sanger Institute Blog

https://sangerinstitute.blog/2016/06/29/companion-a-new-tool-to-generate-and-visualize-annotation-of-parasite-genomes

Wellcome Trust Sanger Institute Blog. Companion: a new tool to generate and visualize annotation of parasite genomes. This entry was posted on June 29, 2016 by sangerinstitute. By Sascha Steinbiss and Thomas D. Otto. What happens if a lot of parasite genomes are generated to fight disease and generate vaccines and drugs, but no one can compare those genomes? However, the problem of generating high quality standardized annotations for these organisms, i.e. locations and functions of genes and othe...A new...

bionics.it

The problem with make for scientific workflows | Bionics IT

http://bionics.it/posts/the-problem-with-make-for-scientific-workflows

The problem with make for scientific workflows. Share this on → Twitter. Posted on: 14 Mar '15. The workflow problem solved once and for all in 1979? UPDATE 2, July 8, 2015:. I should clarify that the problems discussed below do not apply to some ways of working with make such as this interesting method by Pierre Lindenbaum. Where the makefile is generated from an XML description. Written first in the 70's :). You specify the target. Of the desired output, and let make figure out what rules it takes to c...

smallchangebio.wordpress.com

November | 2015 | Small Change Bioinformatics

https://smallchangebio.wordpress.com/2015/11

Monthly Archives: November 2015. November 10, 2015. Notes: Bio in Docker Symposium 2015 day 2: Docker infrastructure and hackathon. I’m at day 2 of the Bio in Docker Symposium. At the Wellcome Collection. In London. This is a great 2 day set of talks and coding sessions around the use of Docker containerization. Notes for day 1. NGS pipelines, workflow tools and data volume management. F1000Research – a publishing platform for the Docker community. Thomas Ingraham and Michael Markie. Allows defining and ...

en.wikipedia.org

Dataflow programming - Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Dataflow_programming

From Wikipedia, the free encyclopedia. By separation of concerns. Is a programming paradigm. That models a program as a directed graph. Of the data flowing between operations, thus implementing dataflow. Principles and architecture. Dataflow programming languages. Share some features of functional languages. And were generally developed in order to bring some functional concepts to a language more suitable for numeric processing. Some authors use the term Datastream instead of Dataflow. Thus, dataflow la...

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Turn on more accessible mode. Turn off more accessible mode. Skip to main content. PLUG N PLAY BRANDING. 160; All Site Content. SharePoint Consulting, Hosting and Branding. Bietet ihnen ein komplett Paket. Ob für private Homepages, Vereine oder auch kleine Unternehmen. Von uns werden sie optimal betreut. Angefangen von der Registrierung ihrer Wunsch Domain und Wunsch Emailadresse, bis hin zum passenden HOSTING Paket inkl. Design und Layout. An ihr ganz persönliches Design anpassen. Try it out now! Und vi...

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Nextflow - A DSL for parallel and scalable computational pipelines

Nextflow is a fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. You can use your favourite programming language. And tools, exploiting your current skills. Just download and play with it. No installation is required. Are you a Python geek or a PERL hacker? You can start fast with it. Lightweight processes with message passing, no shared memory. Develop on your laptop, run in the grid or scale-out in the cloud with no changes.

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NextFlow: An Object-Business Process Mapping Framework

NextFlow: An Object-Business Process Mapping Framework. NextFlow is a mapping framework that supports the representation of business process elements (like process definitions and tasks) using object-oriented abstractions (like interfaces and methods). By using NextFlow, a client system can access a Business Process Management System (BPMS) using traditional OO constructs. NextFlow in a Nutshell. Fig 1 - Hello World Business Process. Process("org.nextflow.sample.helloworld"). This code executes the 'hell...

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