STRMPSWorkflowBatch: Batch wrapper for the workflow function

In svilsen/STRMPS: Analysis of Short Tandem Repeat (STR) Massively Parallel Sequencing (MPS) Data

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.

svilsen/STRMPS documentation built on May 31, 2019, 7:55 a.m.