#' run JAFFA fusion gene detection
#'
#' @param sampleId id for naming the job script
#' @param dataDir location of the fastq files
#' @param filePattern file pattern to include all the relevant fastq files
#' @param projName name of the project
#' @param outDir full path to file output
#'
#' @export
runJAFFA <- function(sampleId, dataDir,filePattern, projName,outDir,
refGenome="hg19",refAnno="genCode19",readLayout="single",
javaMod="compilers/java/1.8.0_40/noarch",
velvetMod="apps/velvet/1.2.10/gcc-4.4.7",
oasesMod="apps/oases/0.2.08/gcc-4.4.7",
blatMod="apps/blat/35/gcc-4.4.7",
samtoolsMod="apps/samtools/0.1.19/gcc-4.4.7",
bowtie2Mod="apps/bowtie2/2.2.1/gcc/4.4.7",
rMod="apps/R/3.3.0/gcc-4.8.5",
jaffaPath="/scratch/pschofield/Projects/Sandbox/JAFFA-version-1.08",
ncores=2,mem="32Gb",noSub=F){
script <- c(
paste0("module load ",javaMod),
paste0("module load ",samtoolsMod),
paste0("module load ",bowtie2Mod),
paste0("module load ",blatMod),
paste0("module load ",velvetMod),
paste0("module load ",oasesMod),
paste0("module load ",rMod),
paste0("mkdir -p ",outDir),
paste0("cd ",outDir),
paste0(file.path(jaffaPath,"tools/bin/bpipe"),
" run -p genome=",refGenome," -p annotation=",refAnno , " -p readLayout=",readLayout,
" ",file.path(jaffaPath,"JAFFA_assembly.groovy"),
" ",file.path(dataDir,filePattern))
)
plib::runScript(jname=paste0("jaffa_",projName,"_",sampleId),jproj=projName,
jdesc=paste0("run of JAFFA fusion transcript detection pipeline "),
jscrp=script,nproc=ncores,mem=mem,noSub=noSub)
}
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