An optional feature of pypiper is the accompanying toolkits, such as the next-gen sequencing toolkit, NGSTk, which simply provides some convenient helper functions to create common commands, like converting from file formats (e.g. bam to fastq), merging files (e.g. merge_bams), counting reads, etc. These make it faster to design bioinformatics pipelines in Pypiper, but are entirely optional.
import pypiper pm = pypiper.PipelineManager(..., args = args) # Create a ngstk object (pass the PipelineManager as an argument) ngstk = pypiper.NGSTk(pm = pm) # Now you use use ngstk functions ngstk.index_bam("sample.bam")
Contributions of additional toolkits or functions in an existing toolkit are welcome.