createSampleSheet_wiki

Running method: createSampleSheet

Overview of createSampleSheet operations

All possible command line arguments for method createSampleSheet:

Argument	Defaults	Description
--bpm	required by user	Full path to bead pool manifest file (.bpm); must be same one used to generate gtc
--gtcDir	required by user	Full path to location of directory/folder containing gtc files to process (files must end in .gtc) -- will not recursively go into sub-directories
--config	required by user	Path and name to configuration file. An example file can be found here.
--outDir	optional, default=current working directory	Full path to directory or folder to output results. If it path does not exist, program will attempt to create it
--logName	optional, default=gtcFuncs.log	Name of log file to output, will be created in directory --outDir
--modDir	optional, default=current working directory	Full path to module files .py from github; default is current working directory with modules folder appended
--sampleSheetUpdates	optional, default=None	Path and name of samplesheet updates. Tab-delimited with following headers required: patientName, DOB, sex, mrn, instrumentID. An example file can be found here.
--fileOutName	optional, default=sampleSheet.csv	Name of final samplesheet file to output, will be created in directory --outDir

The minimum command required to manipulate gtc files is the following:

python3 gtcFuncs.py createSampleSheet --bpm /path/to/manifest.bpm --gtcDir /path/to/gtcLocations/ --config examples/sampleSheet.cfg

Here is an example of how that would look like on the command line:

python3 gtcFuncs.py createSampleSheet --bpm /path/to/manifest.bpm --gtcDir /path/to/gtcLocations/ --outDir /path/to/gtcLocations/ --config examples/sampleSheet.cfg --sampleSheetUpdates updateSampleSheet.txt