R/app-hifiasm.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


ezMethodHifiasm = function(input=NA, output=NA, param=NA, htmlFile="00index.html"){
  opt = param$cmdOptions
  sampleName = input$getNames()
  inputFileType = param$inputType
  if (inputFileType == "HiFi"){
    cmd = paste("hifiasm", "-o", sampleName, 
                paste("-t", ezThreads()), paste("--n-hap", param$ploidy),"--primary", opt, 
                input$getFullPaths("Read1"), 
                "2> ", paste0(sampleName,"_hifiasm.log"))
    ezSystem(cmd, wait = TRUE)
    cmd=paste("awk", "'/^S/{print", paste0('"', '>', '"', '$2;print'), "$3}'", paste0(sampleName, ".p_ctg.gfa"), ">", paste0(sampleName, ".p_ctg.fa"))
    system(cmd, wait = TRUE)
    return("Success")
  }else if (inputFileType == "ONT"){
    cmd = paste("hifiasm", "-o", sampleName, 
                paste("-t", ezThreads()), paste("--n-hap", param$ploidy),"--primary", opt, 
                "--ont", input$getFullPaths("Read1"), 
                "2> ", paste0(sampleName,"_hifiasm.log"))
    ezSystem(cmd, wait = TRUE)
    cmd=paste("awk", "'/^S/{print", paste0('"', '>', '"', '$2;print'), "$3}'", paste0(sampleName, ".p_ctg.gfa"), ">", paste0(sampleName, ".p_ctg.fa"))
    system(cmd, wait = TRUE)
    return("Success")
  }
}

##' @template app-template
##' @templateVar method ezMethodSpades()
##' @templateVar htmlArg )
##' @description Use this reference class to run 
EzAppHifiasm <-
  setRefClass("EzAppHifiasm",
              contains = "EzApp",
              methods = list(
                initialize = function()
                {
                  "Initializes the application using its specific defaults."
                  runMethod <<- ezMethodHifiasm
                  name <<- "EzAppHifiasm"
                  appDefaults <<- rbind(inputType = ezFrame(Type="character",  DefaultValue="HiFi",  Description="PacBio HiFi reads or Oxford Nanopore reads"),
                                        ploidy = ezFrame(Type="integer",  DefaultValue="2",  Description="number of haplotypes"))
                }
              )
)