01_first_snakefile.rst

Hello world!

In this chapter, we show how to create and use RNFtools on a Hello world example. Little knowledge of Python can be helpful, but it is not required.

RNFtools is based on Snakemake, a Python-based Make-like build system. To simulate reads or evaluate alignments, you create simple configuration Python scripts and RNFtools subsequently creates a set of rules to be run by Snakemake. The rules can be then executed in a single thread, in parallel (--cores Snakemake parameter), or on a cluster. For more details about Snakemake, please see its documentation.

This approach allows to create big and reproducible pipelines, which are easy to share (it suffices to publish a single configuration script).

Every RNFtools script consists of three parts:

.. literalinclude:: ../../examples/01_tutorial/01_first_snakefile/Snakefile
        :language: python
        :linenos:

As it is mentioned in the second comment, all your code should be inserted into part 2. Now save this file with name Snakefile and run

snakemake

in the same directory. A "Hello world" message will be printed, together with several Snakemake informative messages.