If here courtesy of Bitbucket or source code, check out the docs online at:
seqpipe, and the package vignette.
seqpipe excels is in separating processing into two distinct phases:
Per Sample Processing - each sample is treated independently, and processing can occur in parallel
Replicate-aware Processing - samples are combined into condition-specific folders such that interdependent samples can be processed together. This is particularly important for ChIP-seq where samples are paired with cognate inputs, and additionally for methods which are designed to consider replicates
Each script (see the Reference page) takes on a specific filetype or step of the process, and is labeled chronologically in alphabetical order, designed to run from A through Z.