etc/gatk-wdl/fm2/tasks/fgi.wdl

   1 version 1.0
   2
   3 task FilterSamReads {
   4         input {
   5                 File inputBam
   6                 File inputBamIndex
   7                 String outputBamPath
   8                 Boolean? createMd5File = false
   9
  10                 Int? compressionLevel
  11
  12                 Int? javaXmxMb = 1024
  13                 Int? memoryMb = javaXmxMb + 512
  14                 # One minute per input gigabyte.
  15                 Int? timeMinutes = 1 + ceil(size(inputBam, "G") * 1)
  16                 String? dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
  17         }
  18         Array[String] FilterScriptContents = [
  19                 'function accept(rec) {'
  20                 '  if (rec.getReadUnmappedFlag()) return false;'
  21                 '  var cigar = rec.getCigar();'
  22                 '  if (cigar == null) return false;'
  23                 '  var readMatch = 0;'
  24                 '  for (var i=0;i < cigar.numCigarElements();++i) {'
  25                 '    var ce = cigar.getCigarElement(i);'
  26                 '    if (ce.getOperator().name() == "M") readMatch += ce.length;'
  27                 '  }'
  28                 '  if (readMatch > 200) return true;'
  29                 '}'
  30                 'accept(record);'
  31         ]
  32
  33         command {
  34                 set -e
  35                 mkdir -p "$(dirname ~{outputBamPath})"
  36                 JAVA_OPTS="-Xmx~{javaXmxMb}M -XX:ParallelGCThreads=1" picard \
  37                 FilterSamReads \
  38                 INPUT=~{sep=' INPUT=' inputBam} \
  39                 OUTPUT=~{outputBamPath} \
  40                 ~{"COMPRESSION_LEVEL=" + compressionLevel} \
  41                 JAVASCRIPT_FILE=${write_lines(FilterScriptContents)} \
  42                 FILTER=includeJavascript \
  43                 CREATE_INDEX=true \
  44                 CREATE_MD5_FILE=~{true="true" false="false" createMd5File}
  45         }
  46
  47         output {
  48                 File outputBam = outputBamPath
  49                 File outputBamIndex = sub(outputBamPath, "\.bam$", ".bai")
  50                 File? outputBamMd5 = outputBamPath + ".md5"
  51         }
  52
  53         runtime {
  54                 memory: "~{memoryMb}M"
  55                 time_minutes: timeMinutes
  56                 #docker: dockerImage
  57         }
  58 }