fastqFileUploadToBaseSpace: once the sraFastqHeaderToIlluminaStandard has been ran on SRA...

In RamsinghLab/arkas_staging: A package that complements Kallisto for quick, informative *seq analysis

Description

once the sraFastqHeaderToIlluminaStandard has been ran on SRA imported samples, the basespace fileupload can be ran. this assumes that a user has a basespace account and has a project directory listed correctly. We assume that the basespace CLI is installed please see (https://help.basespace.illumina.com/articles/descriptive/basespace-cli/). this R interface to BaseSpace cloud system is mostly useful for numerous samples targeting the uses of single cell sequencing with samples ranging from upwards 800; thus making fastq uploading difficult; hence the automation of it within Arkas. Fastq Headers must be in illumina standards. FIX ME: we would also like to add the execution of arkas via the basespace CLI to run cloud applications via R.

Usage

fastqFileUploadToBaseSpace(illuminaDirPath = NULL, illuminafastqFile = NULL,
  basespaceProject = NULL, fastqFileSignature = "_001.fastq.gz",
  illuminaDirs = NULL, paired = FALSE, dryRun = FALSE)

Arguments

illuminaDirPath	a illumina directory path to illumina standard fastq files with illumina header and naming conventions.
illuminafastqFile	fastq files with illumina headers and naming conventions, a vector of file names in illumina standard, this is optional parameter for large directories where hte names are numerious, in this case use the file signature for multi uploads
basespaceProject	character string of the basespace project name, this must exist on basespace
fastqFileSignature	character that is unique to the fastq file directory where upon grep'ing the desired files will get matched. the default is the illumina standard suffix _001.fastq.gz which should pick out the illumina files in the case where the fastq directory has multiple raw files.
illuminaDirs	a character of illumina sample directories which contain illumina fastqs, if SE, only 1 fastq in this dir, if PE, there should be 2 or more.
paired	boolean if the illuminaDirs contains a paired fastq pair
dryRun	boolena if true then for bs CLI will simulate an upload, if false bs CLI will upload a fastq to the real account.

Value

nothing, a successful indication that the files were uploaded to basespace

integer for success or failure

Examples

## Not run: 
fastqFileUploadToBaseSpace(illuminaDirPath,
                          illuminafastqFile=illuminaFastqFiles,
                          basespaceProject=basespaceProject,
                          illuminaDirs=illuminaDirs)

## End(Not run) 

RamsinghLab/arkas_staging documentation built on March 14, 2021, 11:40 a.m.