Computational biology and genomics
An approach I like to use when learning a new tool is to get started by trying to run an example and then gradually work out the details. In this post, I’m trying to learn the basics of the Workflow Description Language (WDL) so that I can adapt GATK workflows for my own use. WDL,…
This is a continuation of my post on getting started with Bpipe. In this post I followed the paired end alignment example from the documentation, with a few adjustments. This pipeline generates a random reference sequence, generates paired end reads from the reference, and aligns these reads back to the reference using BWA.
I have been using simple shell scripts for creating my bioinformatic pipelines. I define variables that can be used as parameter settings throughout the script, use some basic Unix tools for creating my output file names, and simply check the existence of files to see whether a step has been run or not. You can…