From zero to Nextflow, bringing Nanorate (NanoSeq) into a workflow

In the field of cancer research there has been a renewed interest in understanding mutational processes of normal tissue. A variation on duplex sequencing, nanorate sequencing (NanoSeq), allows identification of somatic mutations with a very low error rates ( less than five errors per billion base pairs in single DNA molecules). Analysis of these type of experiments requires a multitude of scripts and programs, written in a diverse set of languages (R, Perl, Python & C++) by two members of the Martincorena group at Sanger. Initially all of this code was organised under one Python wrapper to simplify the analysis. However, it soon became apparent that a third layer of organisation would be necessary in order to turn this code into a workflow capable of handling the large throughput required by researchers. Nextflow seemed to be a natural choice for designing this workflow. I will detail this journey into Nextflow of how a simple DSL1 flow grew into a batch capable DSL2 workflow.