I am no longer working on this repository and have therefore decided to archive it.

Rattle is a collection of opinionated helper functions and classes for running a Snakemake pipeline. It imposes a certain way of structuring input information, with the goal making Snakefiles for next generation sequencing pipelines even more readable.

Rattle was written with next-generation sequencing experiments in minds. As such, it expects that pipeline inputs be organized in a tiered-level of samples (a single unit to be analyzed by the experiment) and read groups (a single unit representing a sequencing run). This is similar to the organization used in BAM files. There, the @RG SM tag corresponds to sample names and @RG ID tag corresponds to read group names.

With that in mind, Rattle expects inputs for Snakemake runs to be organized in a config file with the following pseudoschema:

settings:
    <setting-key-0-name>: <setting-key-0-value>
    <setting-key-n-name>: <setting-key-n-value>
samples:
    <sample-0-name>:
        read_groups:
            <read-group-0-name>:
                <input-0-name>: <path-to-input-0>
                <input-n-name>: <path-to-input-n>
                tags:
                    <key-0-name>: <key-0-value>
                    <key-n-name>: <key-n-value>
    <sample-n-name>:
        read_groups:
            <read-group-0-name>:
                <input-0-name>: <path-to-input-0>
                <input-n-name>: <path-to-input-n>
                tags:
                    <key-0-name>: <key-0-value>
                    <key-n-name>: <key-n-value>

The settings entry as well as tags entry are optional.

Take a look at the test directory to see how Rattle is used.