dxCompiler 2.4.2

• -imports now works correctly - import statements can reference files that are relative to an import directory rather than the main document
• Coercion from Object to Map is now allowed - this enables the result of read_json to be assigned to a variable of type Map
• Strings with escape sequences are now processed correctly - to preserve escape sequences in a string, they need to be "double-escaped"
  • For example, to pass a regular expression containing a tab character to the second argument of the sub function:

    String s1 = "hello\tBob"
    String s2 = sub(s1, "\\t", " ")

  • Another common example is passing a read group to bwa mem. Whether the string is defined in WDL, in a JSON input file, or on the command line, it needs to be "double-escaped":

    String rg = "@RG\\tID:${sample_name}\\tSM:${sample_name}\\tLB:${sample_name}\\tPL:ILLUMINA"
    
    command <<<
    bwa -R "~{rg}" ...
    >>>

• Fixes an issue where indentation is stripped out of some commands
• The default reorg applet now polls the analysis until it is fully updated before proceeding. For custom reorg applets, see the updated code in the example.
• Fixes an issue with nested scatters that reference private variables from outer scopes, e.g.

  workflow wf {
    input {
      Array[String] samples
      Array[File] files
    } 
    scatter (i in range(length(samples))) {
      scatter (j in range(length(files))) {
        call mytask { 
          input: sample = samples[i], file = files[j]
        }
      }  
    }
  }