R/app-canu.R

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

###################################################################
# Functional Genomics Center Zurich
# This code is distributed under the terms of the GNU General
# Public License Version 3, June 2007.
# The terms are available here: http://www.gnu.org/licenses/gpl.html
# www.fgcz.ch


ezMethodCanu = function(input=NA, output=NA, param=NA, htmlFile="00index.html"){
  opt = param$cmdOptions
  sampleName = input$getNames()
  SMRT_Path = input$getFullPaths("Read1")
  SMRT_File = basename(input$getColumn("Read1"))
  inputFileType = param$inputType
  if (inputFileType == "pacbioSmrtCell"){
  ezSystem(paste("cp -r", SMRT_Path, "."))
  ezSystem(paste("mkdir", "smrt_input"))
  ezSystem(paste("tar -zxf", SMRT_File, "--strip-components=4 -C smrt_input"))
  readFile = file.path(getwd(), "smrt_input", "Analysis_Results", "*.subreads.fastq") 
  ezSystem(paste("cat", readFile, ">", paste0(sampleName,".fastq")))
  cmd = paste("canu", "-p", "canu", "-d", "canu", paste0("genomeSize=", param$canuGenomeSize, "k"), paste0("maxMemory=", param$ram), paste0("maxThreads=", ezThreads()), opt, 
                param$canuReadOpt, paste0(sampleName,".fastq"), "1> ", paste0(sampleName,"_canu.log"))
  ezSystem(cmd)
  ezSystem(paste("cp", "canu/canu.contigs.fasta", basename(output$getColumn("Draft"))))
  ezSystem(paste("mv", "canu", sampleName))
  return("Success")
  }else{
    cmd = paste("canu", "-p", sampleName, "-d", sampleName, 
                paste0("genomeSize=", param$canuGenomeSize, "k"), 
                paste0("maxMemory=", param$ram), 
                paste0("maxThreads=", ezThreads()), opt, 
                param$canuReadOpt, input$getFullPaths("Read1"), 
                "1> ", paste0(sampleName,"_canu.log"))
    ezSystem(cmd)
    contigOutputFile <- paste0(sampleName,"/",sampleName,".contigs.fasta")
    ezSystem(paste("cp", contigOutputFile, 
                   basename(output$getColumn("Draft"))))
    return("Success")
  }
}

##' @template app-template
##' @templateVar method ezMethodSpades()
##' @templateVar htmlArg )
##' @description Use this reference class to run 
EzAppCanu <-
  setRefClass("EzAppCanu",
              contains = "EzApp",
              methods = list(
                initialize = function()
                {
                  "Initializes the application using its specific defaults."
                  runMethod <<- ezMethodCanu
                  name <<- "EzAppCanu"
                  appDefaults <<- rbind(canuReadOpt = ezFrame(Type="character",  DefaultValue="-pacbio-raw",  Description="input read types: -pacbio-raw, -pacbio-corrected, -nanopore-raw, -nanopore-corrected. Default is pacbio raw data"),
                                        canuGenomeSize = ezFrame(Type="integer",  DefaultValue="5000",  Description="estimated genome size in Kbp"))
                }
              )
)