Python API/Reference Docs

Modules

rnaseqflow is composed of three modules:

__main__

Provides the entry point for the executable in the function main() and argument parsing in opts()

• function main()
• function opts()

workflow

Provides several classes that are used to execute a series of preprocessing steps on RNAseq data

• class Workflow
• class WorkflowStage
• class FindFiles
• class MergeSplitFiles
• class FastQMCFTrimSolo
• class FastQMCFTrimPairs

cliutils

Provides a class that can intelligently ask the user to provide arguments if the required arguments were not provided at the command line

• class ArgFiller
• function all_subclasses
• function trim
• function firstline