The most atomic unit in MIP is the
command modules and internal sub routines. These modules are ordered in analysis recipes that in turn are assembled into pipeline recipes.
These modules serve as an API for each specific command e.g. "cd", "git clone" or "bwa mem". The command modules are independent, reusable, unit tested and ensure that all interaction with a specific command is recorded, versioned and tested in a single location in MIP. Every module can if supplied with an already opened filehandle write to a file or return an array of the commands depending on the input parameters. They can all write or append to the unix standard streams i.e. STDOUT, STDERR. They are always accompanied by a sub routine test script testing the expected input and output for each parameter to the command modules subroutines.
Recipes are a list of ordered commands and subroutines that has a defined input and output. They are always accompanied by a recipe test script testing the expected input and output and execution of sub routines within the recipe.
They are all located in
lib/MIP/Main/Install.pm to handle installation of programs and references.
lib/MIP/Main/Download.pmto download and prepare references.
lib/MIP/Main/Analyse.pm to build meta datafiles for references.
lib/MIP/Main/Analyse.pm to perform operation with a defined input and output for a process with specific upstream and/or downstream dependencies, e.g. qc of fastqc files or alignment and sorting of reads.
lib/MIP/Recipes/[Pipeline].pm to tie together several analysis recipes into entire pipelines.