Docker on Shaun Chuah https://shaunchuah.github.io/tags/docker/ Recent content in Docker on Shaun Chuah Shaun Chuah https://shaunchuah.github.io/profile_photo.jpg https://shaunchuah.github.io/profile_photo.jpg Hugo -- 0.151.0 en-us Thu, 12 Aug 2021 18:24:45 +0000 How to Create Your Bioinformatics Pipeline with Nextflow https://shaunchuah.github.io/posts/bioinformatics-pipeline-with-nextflow/ Thu, 12 Aug 2021 18:24:45 +0000 https://shaunchuah.github.io/posts/bioinformatics-pipeline-with-nextflow/ <p>Now that you know how to run bioinformatics software in Docker containers, it&rsquo;s time to connect them up. If you&rsquo;ve missed the last post the link is here: <a href="https://shaunchuah.github.io/posts/getting-started-with-docker-for-bioinformatics">Getting started with Docker for bioinformatics.</a></p> <h2 id="content-overview">Content Overview</h2> <ol> <li>What is a pipeline?</li> <li>Nextflow vs Snakemake</li> <li>Using Nextflow and Docker containers to create your pipeline</li> <li>Summary</li> </ol> <h2 id="what-is-a-pipeline-anyway">What is a pipeline anyway?</h2> <p>The term &lsquo;pipeline&rsquo; 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.</p> Getting Started With Docker for Bioinformatics https://shaunchuah.github.io/posts/getting-started-with-docker-for-bioinformatics/ Thu, 05 Aug 2021 18:23:00 +0000 https://shaunchuah.github.io/posts/getting-started-with-docker-for-bioinformatics/ <p>Next generation sequencing is becoming much more accessible to researchers in 2021. As you stare at the freshly minted .fastq files, you&rsquo;re wondering - how do I go about analysing this?</p> <p>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&rsquo;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.</p>