Next Generation Sequencing, GNU-Make and .INTERMEDIATE by Pierre Lindenbaum.
From the post:
I gave a crash course about NGS to a few colleagues today. For my demonstration I wrote a simple Makefile. Basically, it downloads a subset of the human chromosome 22, indexes it with bwa, generates a set of fastqs with wgsim, align the fastqs, generates the *.sai, the *.sam, the *.bam, sorts the bam and calls the SNPs with mpileup.
An illustration that there is plenty of life left in GNU Make.
Plus an interesting tip on the use of .intermediate in make scripts.
As a starting point, consider Make (software).