Modules

• alignment
  • extractUnaligned()
  • runBWA()
  • runGMAP()
  • runHisat2()
  • runMagicBlast()
  • runMinimap2()
  • runSTAR()
  • sortAlignments()
• arguments
• calling
  • filterAS_StrandOddsRatio()
  • runJacusa()
  • runReditools2()
• config
  • loadConfig()
  • setWorkPath()
• cropping
  • detectFilesToCrop()
  • runTrimGalore()
  • runTrimmomatic()
• downloads
  • downloadSRAs()
  • getExperimentsList()
• logger
  • loadConfig()
• quality
  • discardHighError()
  • runFastQC()
  • runQualimap()
• results
  • generateGraphs()
  • mergeCalling()
  • runSnpEff()
• software
  • checkTools()
  • downloadTools()
• util
  • execCmd()
  • makeDirectory()
  • runCommand()
  • runSlurm()
  • stopProgram()
  • sync_annotation_to_fasta()
  • waitForJobs()