Bioinformatics

Why bother setting up another server to manage your Nextflow pipeline? Avoid premature termination of the pipeline. When you run a Nextflow pipeline from your local computer, your local computer is managing the tasks and communicating with Azure as jobs are completed. Depending on the complexity of your pipeline, this may be a long time (couple of days!). If your wi-fi router accidentally comes unplug or the connection is broken, the pipeline will terminate prematurely. While you could recover from this using -resume, you can avoid the risks of disconnection by using a cloud server, which is designed to run 24/7, to orchestrate this. ...

We will cover getting your nextflow pipeline up and running in the cloud using Azure. First thing to note, this process will take some time so sit back, grab a coffee and take your time working through each section. Useful References Nextflow documentation here. Nextflow blog post here. 1. Context Let’s start with some context. I’m working with a small team of immunology researchers who are following their scientific questions which has led into genomics. We don’t have any bioinformatics setup and are starting from nothing - which is probably going to be the case for many newcomers as NGS technology continues to become more accessible (for example Nanopore sequencing). ...

Now that you know how to run bioinformatics software in Docker containers, it’s time to connect them up. If you’ve missed the last post the link is here: Getting started with Docker for bioinformatics. Content Overview What is a pipeline? Nextflow vs Snakemake Using Nextflow and Docker containers to create your pipeline Summary What is a pipeline anyway? The term ‘pipeline’ is thrown around a lot in bioinformatics. In simple terms, it refers to the programs that have to be run in a certain order to complete the analysis. Some of these programs take the outputs of earlier programs and process them in order to achieve a specific objective. ...

Next generation sequencing is becoming much more accessible to researchers in 2021. As you stare at the freshly minted .fastq files, you’re wondering - how do I go about analysing this? After a stint on Google, you decide that you want to run bwa-mem/bowtie2 and then send the output into samtools. Next thing you know, you’re trying to install half a dozen bioinformatic programs on your new ubuntu machine. You run into dependency hell or else conda seems to be stuck solving god knows what and this quickly eats up half your day. ...