STRMPSWorkflowBatch {STRMPS}

Batch wrapper for the workflow function

Description

The function takes an input directory and performs the entire analysis workflow described in (ADD REF). The function creates a series of objects needed for further analyses and stores them at the output location.

Usage

STRMPSWorkflowBatch(input, output, ignorePattern = NULL,
  continueCheckpoint = NULL, control = workflow.control())

Arguments

input

A directory where fastq input-files are stored.

output

A directory where output-files are stored.

ignorePattern

A pattern parsed to grepl used to filter input strings.

continueCheckpoint

Choose a checkpoint to continue from in the workflow. If NULL the function will run the entire workflow.

control

Function controlling non-crucial parameters and other control functions.

Value

If 'output' not provided the function simply returns the stringCoverageList-object. If an output is provided the function will store ALL created objects at the output-path, i.e. nothing is returned.