I want to make a genome assembly workflow, from raw reads to draft genome. ( with Automatic QC/assembly/GapFilling/scaffolding).
For this i took various third party program and i have written some shell script to run one after another.
Now i want to make some user define flexibility with make file and i also want to pass some command line parameter. Can any one suggest me the how to make such a work flow. Which language will be better and some beginners guide how to generate make file
Thank you advance.